HEADER HYDROLASE 25-NOV-15 5EYH
TITLE CRYSTAL STRUCTURE OF IMPASE/NADP PHOSPHATASE COMPLEXED WITH NADP AND
TITLE 2 CA2+ AT PH 7.0
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: INOSITOL MONOPHOSPHATASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: IMPASE/NADP PHOSPHATASE, MYO-INOSITOL-1(OR 4)-
COMPND 5 MONOPHOSPHATASE;
COMPND 6 EC: 3.1.3.25;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS;
SOURCE 3 ORGANISM_TAXID: 1280;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PQE30
KEYWDS IMPASE, FIG SUPERFAMILY, SUBSTRATE BOUND COMPLEX, PHOSPHATASE,
KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.BHATTACHARYYA,D.DUTTA,A.K.GHOSH,A.K.DAS
REVDAT 3 20-MAR-24 5EYH 1 LINK
REVDAT 2 25-JAN-17 5EYH 1 JRNL
REVDAT 1 23-DEC-15 5EYH 0
SPRSDE 23-DEC-15 5EYH 4G64
JRNL AUTH S.BHATTACHARYYA,A.DUTTA,D.DUTTA,A.K.GHOSH,A.K.DAS
JRNL TITL STRUCTURAL ELUCIDATION OF THE NADP(H) PHOSPHATASE ACTIVITY
JRNL TITL 2 OF STAPHYLOCOCCAL DUAL-SPECIFIC IMPASE/NADP(H) PHOSPHATASE
JRNL REF ACTA CRYSTALLOGR D STRUCT V. 72 281 2016
JRNL REF 2 BIOL
JRNL REFN ISSN 2059-7983
JRNL PMID 26894675
JRNL DOI 10.1107/S2059798316000620
REMARK 2
REMARK 2 RESOLUTION. 2.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0073
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.90
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 19318
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.184
REMARK 3 R VALUE (WORKING SET) : 0.181
REMARK 3 FREE R VALUE : 0.242
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1044
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1387
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52
REMARK 3 BIN R VALUE (WORKING SET) : 0.2330
REMARK 3 BIN FREE R VALUE SET COUNT : 77
REMARK 3 BIN FREE R VALUE : 0.2590
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4125
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 113
REMARK 3 SOLVENT ATOMS : 158
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.79
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.12000
REMARK 3 B22 (A**2) : -0.53000
REMARK 3 B33 (A**2) : -1.05000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 1.05000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.803
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.296
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.108
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4403 ; 0.015 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 4136 ; 0.005 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5984 ; 1.842 ; 1.999
REMARK 3 BOND ANGLES OTHERS (DEGREES): 9537 ; 1.068 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 523 ; 7.655 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;40.017 ;25.816
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 761 ;17.026 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;21.746 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 664 ; 0.099 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4881 ; 0.009 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1002 ; 0.004 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2083 ; 2.854 ; 3.734
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2082 ; 2.850 ; 3.734
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2600 ; 4.380 ; 5.588
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NCS TYPE: LOCAL
REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1
REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT
REMARK 3 1 A 4 263 B 4 263 15697 0.090 0.050
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY
REMARK 4
REMARK 4 5EYH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-NOV-15.
REMARK 100 THE DEPOSITION ID IS D_1000215711.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 09-MAR-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20372
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.499
REMARK 200 RESOLUTION RANGE LOW (A) : 75.905
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 7.500
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.09500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8
REMARK 200 DATA REDUNDANCY IN SHELL : 7.40
REMARK 200 R MERGE FOR SHELL (I) : 0.48500
REMARK 200 R SYM FOR SHELL (I) : 0.48500
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP 10.2.35, MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.11
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M CACL2 2H2O, 0.1M HEPES PH 7.0,
REMARK 280 15% (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 30.16550
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 5790 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21200 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 1
REMARK 465 TYR A 264
REMARK 465 ARG A 265
REMARK 465 MET B 1
REMARK 465 THR B 2
REMARK 465 ASP B 3
REMARK 465 HIS B 38
REMARK 465 ARG B 39
REMARK 465 PHE B 40
REMARK 465 ASP B 41
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ARG A 39 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 52 CD OE1 NE2
REMARK 470 TYR A 61 OH
REMARK 470 GLN A 170 NE2
REMARK 470 LYS A 206 NZ
REMARK 470 GLN B 7 CD OE1 NE2
REMARK 470 GLN B 19 CD OE1 NE2
REMARK 470 LYS B 36 CB CG CD CE NZ
REMARK 470 ARG B 37 CD NE CZ NH1 NH2
REMARK 470 LEU B 42 CD1 CD2
REMARK 470 TYR B 61 OH
REMARK 470 ASN B 79 CG OD1 ND2
REMARK 470 GLU B 135 CD OE1 OE2
REMARK 470 PHE B 142 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 LYS B 236 CG CD CE NZ
REMARK 470 ARG B 265 NE CZ NH1 NH2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O HOH B 412 O HOH B 446 1.96
REMARK 500 O PRO B 115 NH1 ARG B 133 2.13
REMARK 500 O PRO A 115 NH1 ARG A 133 2.13
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ILE A 157 CB - CA - C ANGL. DEV. = -12.6 DEGREES
REMARK 500 ILE B 157 CB - CA - C ANGL. DEV. = -12.3 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 LYS A 36 -86.72 -117.15
REMARK 500 HIS A 38 -172.05 -176.18
REMARK 500 GLU A 71 30.57 -97.38
REMARK 500 GLU A 80 60.87 -117.23
REMARK 500 ASN A 204 59.78 -156.37
REMARK 500 LYS B 36 -70.23 -103.28
REMARK 500 GLU B 71 32.48 -98.50
REMARK 500 GLU B 80 58.20 -115.23
REMARK 500 ASN B 204 61.43 -156.09
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 GLY A 237 ALA A 238 145.25
REMARK 500 GLY B 237 ALA B 238 145.24
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 301 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 70 OE2
REMARK 620 2 ASP A 88 OD1 99.1
REMARK 620 3 ASP A 88 OD2 97.4 46.5
REMARK 620 4 ILE A 90 O 160.6 75.3 92.0
REMARK 620 5 NAP A 306 O3X 101.0 112.4 67.3 98.3
REMARK 620 6 NAP A 306 O3X 109.7 111.1 68.3 89.5 8.8
REMARK 620 7 HOH A 406 O 83.9 89.6 135.9 77.5 156.0 152.1
REMARK 620 8 HOH A 408 O 83.9 166.1 146.9 97.4 80.0 80.1 77.2
REMARK 620 N 1 2 3 4 5 6 7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 302 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 70 OE1
REMARK 620 2 NAP A 306 O1X 108.0
REMARK 620 3 NAP A 306 O1X 102.4 6.6
REMARK 620 4 HOH A 408 O 98.2 82.8 80.0
REMARK 620 5 HOH A 409 O 79.6 140.9 137.6 58.1
REMARK 620 6 HOH A 422 O 109.4 133.8 140.3 117.0 72.6
REMARK 620 7 HOH A 426 O 173.7 67.0 72.3 77.6 101.8 76.8
REMARK 620 8 HOH A 459 O 87.1 77.0 79.8 159.8 142.0 78.8 95.3
REMARK 620 N 1 2 3 4 5 6 7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 305 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 88 OD2
REMARK 620 2 ASP A 91 OD1 106.3
REMARK 620 3 ASP A 209 OD1 117.0 111.4
REMARK 620 4 NAP A 306 O3X 84.5 104.8 128.7
REMARK 620 5 NAP A 306 O3X 85.6 95.5 136.0 9.4
REMARK 620 6 NAP A 306 O2B 147.7 83.5 85.8 63.2 62.5
REMARK 620 7 NAP A 306 O2B 144.4 83.8 88.8 60.0 59.2 3.4
REMARK 620 8 HOH A 414 O 107.3 145.3 59.0 70.4 78.8 63.4 63.7
REMARK 620 N 1 2 3 4 5 6 7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 302 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU B 70 OE1
REMARK 620 2 ASP B 88 OD1 106.7
REMARK 620 3 ASP B 88 OD2 95.5 46.0
REMARK 620 4 ILE B 90 O 171.8 77.3 92.4
REMARK 620 5 NAP B 303 O2X 91.1 113.7 69.6 93.7
REMARK 620 6 HOH B 418 O 91.5 88.3 133.8 81.4 156.0
REMARK 620 7 HOH B 423 O 74.1 171.4 142.5 100.8 74.7 83.1
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA B 301 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 88 OD2
REMARK 620 2 ASP B 91 OD1 96.4
REMARK 620 3 ASP B 209 OD1 117.8 102.7
REMARK 620 4 NAP B 303 O2B 142.4 80.2 99.3
REMARK 620 5 NAP B 303 O2X 85.7 95.4 147.9 57.8
REMARK 620 6 HOH B 439 O 102.5 159.2 76.1 79.6 77.6
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NAP B 303
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5EYG RELATED DB: PDB
DBREF1 5EYH A 1 265 UNP A0A0D6HL44_STAAU
DBREF2 5EYH A A0A0D6HL44 1 265
DBREF1 5EYH B 1 265 UNP A0A0D6HL44_STAAU
DBREF2 5EYH B A0A0D6HL44 1 265
SEQADV 5EYH PHE A 142 UNP A0A0D6HL4 ILE 142 ENGINEERED MUTATION
SEQADV 5EYH PHE B 142 UNP A0A0D6HL4 ILE 142 ENGINEERED MUTATION
SEQRES 1 A 265 MET THR ASP LYS THR LEU GLN GLN ILE ASP LYS LEU ILE
SEQRES 2 A 265 CYS SER TRP LEU LYS GLN ILE ASP ASN VAL ILE PRO GLN
SEQRES 3 A 265 LEU ILE MET GLU MET THR THR GLU THR LYS ARG HIS ARG
SEQRES 4 A 265 PHE ASP LEU VAL THR ASN VAL ASP LYS GLN ILE GLN GLN
SEQRES 5 A 265 GLN PHE GLN GLN PHE LEU ALA THR TYR PHE PRO GLU HIS
SEQRES 6 A 265 GLN LEU LEU ALA GLU GLU LYS SER ASN ALA MET ILE THR
SEQRES 7 A 265 ASN GLU ILE ASN HIS LEU TRP ILE MET ASP PRO ILE ASP
SEQRES 8 A 265 GLY THR ALA ASN LEU VAL LYS GLN GLN GLU ASP TYR CYS
SEQRES 9 A 265 ILE ILE LEU ALA TYR PHE TYR GLU GLY LYS PRO MET LEU
SEQRES 10 A 265 SER TYR VAL TYR ASP TYR PRO HIS LYS LYS LEU TYR LYS
SEQRES 11 A 265 ALA ILE ARG GLY GLU GLY ALA PHE CYS ASN GLY PHE LYS
SEQRES 12 A 265 MET GLU GLU PRO PRO SER LEU LYS LEU GLU ASP ALA ILE
SEQRES 13 A 265 ILE SER PHE ASN ALA GLN VAL MET ASN LEU ASP THR VAL
SEQRES 14 A 265 GLN ASP LEU PHE ASP ALA SER PHE SER TYR ARG LEU VAL
SEQRES 15 A 265 GLY ALA CYS GLY LEU ASP SER MET ARG VAL ALA LYS GLY
SEQRES 16 A 265 GLN PHE GLY ALA HIS ILE ASN THR ASN PRO LYS PRO TRP
SEQRES 17 A 265 ASP ILE ALA ALA GLN PHE LEU PHE ALA GLU LEU LEU ASN
SEQRES 18 A 265 LEU LYS MET THR THR LEU ASP GLY LYS ALA ILE ASP HIS
SEQRES 19 A 265 LEU LYS GLY ALA PRO PHE ILE ILE SER ASN LYS ALA CYS
SEQRES 20 A 265 HIS GLU THR VAL LEU LYS ILE LEU ASN ALA ASN GLY GLY
SEQRES 21 A 265 TYR GLN LYS TYR ARG
SEQRES 1 B 265 MET THR ASP LYS THR LEU GLN GLN ILE ASP LYS LEU ILE
SEQRES 2 B 265 CYS SER TRP LEU LYS GLN ILE ASP ASN VAL ILE PRO GLN
SEQRES 3 B 265 LEU ILE MET GLU MET THR THR GLU THR LYS ARG HIS ARG
SEQRES 4 B 265 PHE ASP LEU VAL THR ASN VAL ASP LYS GLN ILE GLN GLN
SEQRES 5 B 265 GLN PHE GLN GLN PHE LEU ALA THR TYR PHE PRO GLU HIS
SEQRES 6 B 265 GLN LEU LEU ALA GLU GLU LYS SER ASN ALA MET ILE THR
SEQRES 7 B 265 ASN GLU ILE ASN HIS LEU TRP ILE MET ASP PRO ILE ASP
SEQRES 8 B 265 GLY THR ALA ASN LEU VAL LYS GLN GLN GLU ASP TYR CYS
SEQRES 9 B 265 ILE ILE LEU ALA TYR PHE TYR GLU GLY LYS PRO MET LEU
SEQRES 10 B 265 SER TYR VAL TYR ASP TYR PRO HIS LYS LYS LEU TYR LYS
SEQRES 11 B 265 ALA ILE ARG GLY GLU GLY ALA PHE CYS ASN GLY PHE LYS
SEQRES 12 B 265 MET GLU GLU PRO PRO SER LEU LYS LEU GLU ASP ALA ILE
SEQRES 13 B 265 ILE SER PHE ASN ALA GLN VAL MET ASN LEU ASP THR VAL
SEQRES 14 B 265 GLN ASP LEU PHE ASP ALA SER PHE SER TYR ARG LEU VAL
SEQRES 15 B 265 GLY ALA CYS GLY LEU ASP SER MET ARG VAL ALA LYS GLY
SEQRES 16 B 265 GLN PHE GLY ALA HIS ILE ASN THR ASN PRO LYS PRO TRP
SEQRES 17 B 265 ASP ILE ALA ALA GLN PHE LEU PHE ALA GLU LEU LEU ASN
SEQRES 18 B 265 LEU LYS MET THR THR LEU ASP GLY LYS ALA ILE ASP HIS
SEQRES 19 B 265 LEU LYS GLY ALA PRO PHE ILE ILE SER ASN LYS ALA CYS
SEQRES 20 B 265 HIS GLU THR VAL LEU LYS ILE LEU ASN ALA ASN GLY GLY
SEQRES 21 B 265 TYR GLN LYS TYR ARG
HET CA A 301 1
HET CA A 302 1
HET GOL A 303 6
HET GOL A 304 6
HET CA A 305 1
HET NAP A 306 96
HET CA B 301 1
HET CA B 302 1
HET NAP B 303 48
HETNAM CA CALCIUM ION
HETNAM GOL GLYCEROL
HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
FORMUL 3 CA 5(CA 2+)
FORMUL 5 GOL 2(C3 H8 O3)
FORMUL 8 NAP 2(C21 H28 N7 O17 P3)
FORMUL 12 HOH *158(H2 O)
HELIX 1 AA1 THR A 5 GLU A 30 1 26
HELIX 2 AA2 ASN A 45 PHE A 62 1 18
HELIX 3 AA3 GLY A 92 GLN A 100 1 9
HELIX 4 AA4 LYS A 151 ASP A 154 5 4
HELIX 5 AA5 ASN A 165 SER A 176 1 12
HELIX 6 AA6 ALA A 184 LYS A 194 1 11
HELIX 7 AA7 LYS A 206 ALA A 211 1 6
HELIX 8 AA8 ALA A 212 LEU A 220 1 9
HELIX 9 AA9 CYS A 247 ALA A 257 1 11
HELIX 10 AB1 THR B 5 GLU B 30 1 26
HELIX 11 AB2 ASN B 45 PHE B 62 1 18
HELIX 12 AB3 GLY B 92 GLN B 100 1 9
HELIX 13 AB4 LYS B 151 ASP B 154 5 4
HELIX 14 AB5 ASN B 165 SER B 176 1 12
HELIX 15 AB6 ALA B 184 LYS B 194 1 11
HELIX 16 AB7 LYS B 206 ALA B 211 1 6
HELIX 17 AB8 ALA B 212 LEU B 220 1 9
HELIX 18 AB9 CYS B 247 ALA B 257 1 11
SHEET 1 AA1 2 THR A 33 THR A 35 0
SHEET 2 AA1 2 LEU A 42 THR A 44 -1 O VAL A 43 N GLU A 34
SHEET 1 AA2 7 GLN A 66 ALA A 69 0
SHEET 2 AA2 7 HIS A 83 ASP A 91 1 O TRP A 85 N LEU A 68
SHEET 3 AA2 7 CYS A 104 TYR A 111 -1 O CYS A 104 N ASP A 91
SHEET 4 AA2 7 LYS A 114 ASP A 122 -1 O LEU A 117 N TYR A 109
SHEET 5 AA2 7 LYS A 127 ILE A 132 -1 O LYS A 127 N ASP A 122
SHEET 6 AA2 7 GLY A 136 CYS A 139 -1 O PHE A 138 N LYS A 130
SHEET 7 AA2 7 PHE A 142 MET A 144 -1 O PHE A 142 N CYS A 139
SHEET 1 AA3 5 SER A 178 TYR A 179 0
SHEET 2 AA3 5 ILE A 156 SER A 158 1 N ILE A 157 O SER A 178
SHEET 3 AA3 5 ALA A 199 ASN A 202 1 O ILE A 201 N SER A 158
SHEET 4 AA3 5 PHE A 240 SER A 243 -1 O PHE A 240 N ASN A 202
SHEET 5 AA3 5 LYS A 223 THR A 226 -1 N LYS A 223 O SER A 243
SHEET 1 AA4 2 THR B 33 GLU B 34 0
SHEET 2 AA4 2 VAL B 43 THR B 44 -1 O VAL B 43 N GLU B 34
SHEET 1 AA5 7 GLN B 66 ALA B 69 0
SHEET 2 AA5 7 HIS B 83 ASP B 91 1 O TRP B 85 N LEU B 68
SHEET 3 AA5 7 CYS B 104 TYR B 111 -1 O CYS B 104 N ASP B 91
SHEET 4 AA5 7 LYS B 114 ASP B 122 -1 O LEU B 117 N TYR B 109
SHEET 5 AA5 7 LYS B 127 ILE B 132 -1 O LYS B 127 N ASP B 122
SHEET 6 AA5 7 GLY B 136 CYS B 139 -1 O PHE B 138 N LYS B 130
SHEET 7 AA5 7 PHE B 142 MET B 144 -1 O MET B 144 N ALA B 137
SHEET 1 AA6 5 SER B 178 TYR B 179 0
SHEET 2 AA6 5 ILE B 156 SER B 158 1 N ILE B 157 O SER B 178
SHEET 3 AA6 5 ALA B 199 ASN B 202 1 O ILE B 201 N SER B 158
SHEET 4 AA6 5 PHE B 240 SER B 243 -1 O PHE B 240 N ASN B 202
SHEET 5 AA6 5 LYS B 223 THR B 226 -1 N LYS B 223 O SER B 243
LINK OE2 GLU A 70 CA CA A 301 1555 1555 2.10
LINK OE1 GLU A 70 CA CA A 302 1555 1555 2.33
LINK OD1 ASP A 88 CA CA A 301 1555 1555 2.26
LINK OD2 ASP A 88 CA CA A 301 1555 1555 2.95
LINK OD2 ASP A 88 CA CA A 305 1555 1555 2.22
LINK O ILE A 90 CA CA A 301 1555 1555 2.28
LINK OD1 ASP A 91 CA CA A 305 1555 1555 2.27
LINK OD1 ASP A 209 CA CA A 305 1555 1555 2.15
LINK CA CA A 301 O3XANAP A 306 1555 1555 2.23
LINK CA CA A 301 O3XBNAP A 306 1555 1555 2.32
LINK CA CA A 301 O HOH A 406 1555 1555 2.37
LINK CA CA A 301 O HOH A 408 1555 1555 2.38
LINK CA CA A 302 O1XANAP A 306 1555 1555 2.40
LINK CA CA A 302 O1XBNAP A 306 1555 1555 2.24
LINK CA CA A 302 O HOH A 408 1555 1555 2.41
LINK CA CA A 302 O HOH A 409 1555 1555 2.90
LINK CA CA A 302 O HOH A 422 1555 1555 2.29
LINK CA CA A 302 O HOH A 426 1555 1555 2.54
LINK CA CA A 302 O HOH A 459 1555 1555 2.29
LINK CA CA A 305 O3XANAP A 306 1555 1555 2.14
LINK CA CA A 305 O3XBNAP A 306 1555 1555 2.20
LINK CA CA A 305 O2BANAP A 306 1555 1555 2.45
LINK CA CA A 305 O2BBNAP A 306 1555 1555 2.57
LINK CA CA A 305 O HOH A 414 1555 1555 3.19
LINK OE1 GLU B 70 CA CA B 302 1555 1555 2.44
LINK OD2 ASP B 88 CA CA B 301 1555 1555 2.33
LINK OD1 ASP B 88 CA CA B 302 1555 1555 2.24
LINK OD2 ASP B 88 CA CA B 302 1555 1555 3.05
LINK O ILE B 90 CA CA B 302 1555 1555 2.40
LINK OD1 ASP B 91 CA CA B 301 1555 1555 2.54
LINK OD1 ASP B 209 CA CA B 301 1555 1555 2.05
LINK CA CA B 301 O2B NAP B 303 1555 1555 2.49
LINK CA CA B 301 O2X NAP B 303 1555 1555 2.28
LINK CA CA B 301 O HOH B 439 1555 1555 2.72
LINK CA CA B 302 O2X NAP B 303 1555 1555 2.37
LINK CA CA B 302 O HOH B 418 1555 1555 2.33
LINK CA CA B 302 O HOH B 423 1555 1555 2.11
SITE 1 AC1 6 GLU A 70 ASP A 88 ILE A 90 NAP A 306
SITE 2 AC1 6 HOH A 406 HOH A 408
SITE 1 AC2 7 GLU A 70 NAP A 306 HOH A 408 HOH A 409
SITE 2 AC2 7 HOH A 422 HOH A 426 HOH A 459
SITE 1 AC3 2 THR A 35 LYS A 36
SITE 1 AC4 7 PHE A 173 ASP A 174 SER A 176 PHE A 177
SITE 2 AC4 7 HOH A 451 GLN B 162 HOH B 407
SITE 1 AC5 4 ASP A 88 ASP A 91 ASP A 209 NAP A 306
SITE 1 AC6 37 HIS A 38 PHE A 40 GLU A 70 ASP A 88
SITE 2 AC6 37 ILE A 90 ASP A 91 GLY A 92 THR A 93
SITE 3 AC6 37 ALA A 94 ASN A 160 GLN A 162 VAL A 163
SITE 4 AC6 37 GLY A 183 ALA A 184 CYS A 185 ASN A 202
SITE 5 AC6 37 THR A 203 ASN A 204 ASP A 209 CA A 301
SITE 6 AC6 37 CA A 302 CA A 305 HOH A 401 HOH A 402
SITE 7 AC6 37 HOH A 405 HOH A 408 HOH A 414 HOH A 425
SITE 8 AC6 37 HOH A 426 HOH A 459 PHE B 173 ASP B 174
SITE 9 AC6 37 SER B 176 PHE B 177 SER B 178 ARG B 180
SITE 10 AC6 37 HOH B 415
SITE 1 AC7 5 ASP B 88 ASP B 91 ASP B 209 NAP B 303
SITE 2 AC7 5 HOH B 439
SITE 1 AC8 6 GLU B 70 ASP B 88 ILE B 90 NAP B 303
SITE 2 AC8 6 HOH B 418 HOH B 423
SITE 1 AC9 28 SER A 178 ARG A 180 GLU B 70 ASP B 88
SITE 2 AC9 28 ILE B 90 ASP B 91 GLY B 92 THR B 93
SITE 3 AC9 28 ALA B 94 ASN B 160 VAL B 163 GLY B 183
SITE 4 AC9 28 CYS B 185 ASN B 202 THR B 203 ASN B 204
SITE 5 AC9 28 ASP B 209 CA B 301 CA B 302 HOH B 403
SITE 6 AC9 28 HOH B 404 HOH B 407 HOH B 411 HOH B 413
SITE 7 AC9 28 HOH B 419 HOH B 420 HOH B 423 HOH B 434
CRYST1 64.505 60.331 79.939 90.00 108.28 90.00 P 1 21 1 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.015503 0.000000 0.005121 0.00000
SCALE2 0.000000 0.016575 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013174 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
