HEADER HYDROLASE 01-SEP-11 3VHQ
TITLE CRYSTAL STRUCTURE OF THE CA6 SITE MUTANT OF PRO-SA-SUBTILISIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TK-SUBTILISIN;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.4.21.62;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS;
SOURCE 3 ORGANISM_TAXID: 69014;
SOURCE 4 STRAIN: KOD1;
SOURCE 5 GENE: TK1675;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)
KEYWDS HYDROLASE, PROTEOLYSIS
EXPDTA X-RAY DIFFRACTION
AUTHOR R.UEHARA,Y.TAKEUCHI,S.TANAKA,H.MATSUMURA,Y.KOGA,K.TAKANO,S.KANAYA
REVDAT 1 11-JUL-12 3VHQ 0
JRNL AUTH R.UEHARA,Y.TAKEUCHI,S.I.TANAKA,K.TAKANO,Y.KOGA,S.KANAYA
JRNL TITL REQUIREMENT OF CA(2+) IONS FOR THE HYPERTHERMOSTABILITY OF
JRNL TITL 2 TK-SUBTILISIN FROM THERMOCOCCUS KODAKARENSIS
JRNL REF BIOCHEMISTRY V. 51 5369 2012
JRNL REFN ISSN 0006-2960
JRNL PMID 22686281
JRNL DOI 10.1021/BI300427U
REMARK 2
REMARK 2 RESOLUTION. 2.15 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0110
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.08
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8
REMARK 3 NUMBER OF REFLECTIONS : 21552
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) : 0.175
REMARK 3 R VALUE (WORKING SET) : 0.171
REMARK 3 FREE R VALUE : 0.241
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1163
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) : 2.15
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1306
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.85
REMARK 3 BIN R VALUE (WORKING SET) : 0.2250
REMARK 3 BIN FREE R VALUE SET COUNT : 74
REMARK 3 BIN FREE R VALUE : 0.3450
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2830
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 5
REMARK 3 SOLVENT ATOMS : 263
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.62
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : 0.00000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.202
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.170
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2889 ; 0.023 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3950 ; 1.973 ; 1.955
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 382 ; 6.800 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;39.226 ;25.357
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 427 ;18.398 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;17.494 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 461 ; 0.155 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2194 ; 0.010 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
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): 1904 ; 1.097 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3063 ; 1.951 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 985 ; 3.165 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 887 ; 4.912 ; 4.500
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 NUMBER OF DIFFERENT NCS GROUPS : NULL
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 : 1.40
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
REMARK 4
REMARK 4 3VHQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-SEP-11.
REMARK 100 THE RCSB ID CODE IS RCSB095058.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 29-MAY-08
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL38B1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : MIRRORS
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24074
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16
REMARK 200 COMPLETENESS FOR SHELL (%) : 78.1
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.95
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 4.0M SODIUM FORMATE, PH 7.0, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X,Y,-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2
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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.71700
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.39000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 62.13950
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.71700
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.39000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 62.13950
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.71700
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.39000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 62.13950
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.71700
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.39000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 62.13950
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 608 LIES ON A SPECIAL POSITION.
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 GLY A 1
REMARK 465 GLU A 2
REMARK 465 GLN A 3
REMARK 465 LEU A 75
REMARK 465 GLY A 76
REMARK 465 GLY A 77
REMARK 465 GLY A 78
REMARK 465 SER A 79
REMARK 465 THR A 80
REMARK 465 GLN A 81
REMARK 465 GLY A 374
REMARK 465 PRO A 375
REMARK 465 THR A 376
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 ALA A 83 -176.42 -66.81
REMARK 500 SER A 105 46.76 -80.07
REMARK 500 ASP A 115 -155.41 -166.01
REMARK 500 ALA A 162 15.18 -141.29
REMARK 500 ASN A 166 -151.37 -163.37
REMARK 500 VAL A 170 -163.12 -124.29
REMARK 500 ILE A 219 -77.26 -129.43
REMARK 500 SER A 271 173.59 -57.70
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 VAL A 22 24.6 L L OUTSIDE RANGE
REMARK 500 VAL A 351 21.1 L L OUTSIDE RANGE
REMARK 500 ILE A 357 24.3 L L OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 619 DISTANCE = 6.24 ANGSTROMS
REMARK 525 HOH A 626 DISTANCE = 6.54 ANGSTROMS
REMARK 525 HOH A 656 DISTANCE = 5.50 ANGSTROMS
REMARK 525 HOH A 657 DISTANCE = 5.63 ANGSTROMS
REMARK 525 HOH A 666 DISTANCE = 7.33 ANGSTROMS
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 402 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 VAL A 170 O
REMARK 620 2 GLN A 84 OE1 82.3
REMARK 620 3 ILE A 168 O 104.4 89.9
REMARK 620 4 ASN A 166 OD1 163.9 81.7 77.3
REMARK 620 5 LEU A 164 O 80.4 78.5 166.9 94.7
REMARK 620 6 ASP A 124 OD1 118.6 155.5 96.3 76.6 91.8
REMARK 620 7 ASP A 124 OD2 76.5 155.9 84.4 119.5 108.7 48.6
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 400 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 208 OD1
REMARK 620 2 ASP A 226 OD2 104.3
REMARK 620 3 VAL A 210 O 89.5 165.8
REMARK 620 4 HOH A 406 O 162.7 92.8 73.6
REMARK 620 5 LEU A 205 O 95.4 89.2 85.9 87.1
REMARK 620 6 HOH A 578 O 86.1 91.6 92.9 91.2 178.1
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 401 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 222 OD1
REMARK 620 2 ILE A 218 O 88.6
REMARK 620 3 ASP A 212 OD1 175.6 93.4
REMARK 620 4 ASP A 225 OD2 87.6 82.6 96.5
REMARK 620 5 ASP A 214 OD2 96.6 172.5 81.1 102.9
REMARK 620 6 ASP A 216 OD1 95.8 86.9 80.4 168.8 87.3
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 399 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 VAL A 108 O
REMARK 620 2 ALA A 227 O 157.8
REMARK 620 3 GLU A 229 OE1 84.9 89.3
REMARK 620 4 GLN A 110 OE1 88.8 83.9 145.7
REMARK 620 5 HOH A 420 O 89.5 110.4 130.4 83.1
REMARK 620 6 GLU A 229 OE2 71.4 87.7 55.8 90.3 159.9
REMARK 620 7 HOH A 413 O 113.3 84.0 67.8 143.9 69.7 122.9
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 403 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 216 OD2
REMARK 620 2 ASP A 214 OD1 88.3
REMARK 620 3 ASP A 222 OD1 82.4 96.1
REMARK 620 4 ASP A 224 OD2 157.7 79.4 117.1
REMARK 620 5 ASP A 222 OD2 120.5 122.0 47.9 81.7
REMARK 620 N 1 2 3 4
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 399
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 400
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 403
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2E1P RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF UNAUTOPROCESSED FORM2 OF TK-SUBTILISIN
REMARK 900 RELATED ID: 2ZWO RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE CA2 SITE MUTANT OF PRO-SA-
REMARK 900 SUBTILISIN
REMARK 900 RELATED ID: 2ZWP RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE CA3 SITE MUTANT OF PRO-SA-
REMARK 900 SUBTILISIN
DBREF 3VHQ A 1 398 UNP P58502 TKSU_PYRKO 25 422
SEQADV 3VHQ ALA A 324 UNP P58502 SER 348 ENGINEERED MUTATION
SEQADV 3VHQ ALA A 372 UNP P58502 ASP 396 ENGINEERED MUTATION
SEQRES 1 A 398 GLY GLU GLN ASN THR ILE ARG VAL ILE VAL SER VAL ASP
SEQRES 2 A 398 LYS ALA LYS PHE ASN PRO HIS GLU VAL LEU GLY ILE GLY
SEQRES 3 A 398 GLY HIS ILE VAL TYR GLN PHE LYS LEU ILE PRO ALA VAL
SEQRES 4 A 398 VAL VAL ASP VAL PRO ALA ASN ALA VAL GLY LYS LEU LYS
SEQRES 5 A 398 LYS MET PRO GLY VAL GLU LYS VAL GLU PHE ASP HIS GLN
SEQRES 6 A 398 ALA VAL LEU LEU GLY LYS PRO SER TRP LEU GLY GLY GLY
SEQRES 7 A 398 SER THR GLN PRO ALA GLN THR ILE PRO TRP GLY ILE GLU
SEQRES 8 A 398 ARG VAL LYS ALA PRO SER VAL TRP SER ILE THR ASP GLY
SEQRES 9 A 398 SER VAL SER VAL ILE GLN VAL ALA VAL LEU ASP THR GLY
SEQRES 10 A 398 VAL ASP TYR ASP HIS PRO ASP LEU ALA ALA ASN ILE ALA
SEQRES 11 A 398 TRP CYS VAL SER THR LEU ARG GLY LYS VAL SER THR LYS
SEQRES 12 A 398 LEU ARG ASP CYS ALA ASP GLN ASN GLY HIS GLY THR HIS
SEQRES 13 A 398 VAL ILE GLY THR ILE ALA ALA LEU ASN ASN ASP ILE GLY
SEQRES 14 A 398 VAL VAL GLY VAL ALA PRO GLY VAL GLN ILE TYR SER VAL
SEQRES 15 A 398 ARG VAL LEU ASP ALA ARG GLY SER GLY SER TYR SER ASP
SEQRES 16 A 398 ILE ALA ILE GLY ILE GLU GLN ALA ILE LEU GLY PRO ASP
SEQRES 17 A 398 GLY VAL ALA ASP LYS ASP GLY ASP GLY ILE ILE ALA GLY
SEQRES 18 A 398 ASP PRO ASP ASP ASP ALA ALA GLU VAL ILE SER MET SER
SEQRES 19 A 398 LEU GLY GLY PRO ALA ASP ASP SER TYR LEU TYR ASP MET
SEQRES 20 A 398 ILE ILE GLN ALA TYR ASN ALA GLY ILE VAL ILE VAL ALA
SEQRES 21 A 398 ALA SER GLY ASN GLU GLY ALA PRO SER PRO SER TYR PRO
SEQRES 22 A 398 ALA ALA TYR PRO GLU VAL ILE ALA VAL GLY ALA ILE ASP
SEQRES 23 A 398 SER ASN ASP ASN ILE ALA SER PHE SER ASN ARG GLN PRO
SEQRES 24 A 398 GLU VAL SER ALA PRO GLY VAL ASP ILE LEU SER THR TYR
SEQRES 25 A 398 PRO ASP ASP SER TYR GLU THR LEU MET GLY THR ALA MET
SEQRES 26 A 398 ALA THR PRO HIS VAL SER GLY VAL VAL ALA LEU ILE GLN
SEQRES 27 A 398 ALA ALA TYR TYR GLN LYS TYR GLY LYS ILE LEU PRO VAL
SEQRES 28 A 398 GLY THR PHE ASP ASP ILE SER LYS ASN THR VAL ARG GLY
SEQRES 29 A 398 ILE LEU HIS ILE THR ALA ASP ALA LEU GLY PRO THR GLY
SEQRES 30 A 398 TRP ASP ALA ASP TYR GLY TYR GLY VAL VAL ARG ALA ALA
SEQRES 31 A 398 LEU ALA VAL GLN ALA ALA LEU GLY
HET CA A 399 1
HET CA A 400 1
HET CA A 401 1
HET CA A 402 1
HET CA A 403 1
HETNAM CA CALCIUM ION
FORMUL 2 CA 5(CA 2+)
FORMUL 7 HOH *263(H2 O)
HELIX 1 1 ASN A 18 ILE A 25 1 8
HELIX 2 2 ALA A 47 LYS A 53 1 7
HELIX 3 3 PRO A 87 VAL A 93 1 7
HELIX 4 4 ALA A 95 TRP A 99 5 5
HELIX 5 5 LEU A 125 ALA A 127 5 3
HELIX 6 6 LEU A 136 LYS A 139 5 4
HELIX 7 7 LYS A 143 ALA A 148 1 6
HELIX 8 8 GLY A 152 ALA A 163 1 12
HELIX 9 9 TYR A 193 GLY A 206 1 14
HELIX 10 10 ASP A 241 ALA A 254 1 14
HELIX 11 11 GLY A 322 TYR A 345 1 24
HELIX 12 12 THR A 361 ALA A 370 1 10
HELIX 13 13 ARG A 388 GLY A 398 1 11
SHEET 1 A 4 HIS A 28 GLN A 32 0
SHEET 2 A 4 ALA A 38 PRO A 44 -1 O VAL A 40 N TYR A 31
SHEET 3 A 4 THR A 5 VAL A 12 -1 N ILE A 6 O VAL A 43
SHEET 4 A 4 VAL A 57 PHE A 62 -1 O LYS A 59 N SER A 11
SHEET 1 B 3 SER A 190 SER A 192 0
SHEET 2 B 3 GLN A 65 LEU A 68 -1 N ALA A 66 O GLY A 191
SHEET 3 B 3 LEU A 235 GLY A 236 -1 O GLY A 236 N VAL A 67
SHEET 1 C 3 LYS A 71 PRO A 72 0
SHEET 2 C 3 SER A 316 MET A 321 -1 O MET A 321 N LYS A 71
SHEET 3 C 3 ILE A 308 TYR A 312 -1 N ILE A 308 O LEU A 320
SHEET 1 D 7 ILE A 129 SER A 134 0
SHEET 2 D 7 GLN A 178 ARG A 183 1 O ARG A 183 N VAL A 133
SHEET 3 D 7 GLN A 110 ASP A 115 1 N VAL A 113 O VAL A 182
SHEET 4 D 7 VAL A 230 MET A 233 1 O VAL A 230 N ALA A 112
SHEET 5 D 7 VAL A 257 ALA A 261 1 O VAL A 259 N MET A 233
SHEET 6 D 7 VAL A 279 ILE A 285 1 O ILE A 280 N ALA A 260
SHEET 7 D 7 VAL A 301 PRO A 304 1 O VAL A 301 N GLY A 283
SSBOND 1 CYS A 132 CYS A 147 1555 1555 2.13
LINK O VAL A 170 CA CA A 402 1555 1555 2.15
LINK OD1 ASP A 208 CA CA A 400 1555 1555 2.18
LINK OD2 ASP A 226 CA CA A 400 1555 1555 2.19
LINK O VAL A 210 CA CA A 400 1555 1555 2.22
LINK CA CA A 400 O HOH A 406 1555 1555 2.23
LINK OD1 ASP A 222 CA CA A 401 1555 1555 2.23
LINK O VAL A 108 CA CA A 399 1555 1555 2.25
LINK OE1 GLN A 84 CA CA A 402 1555 1555 2.28
LINK O ILE A 218 CA CA A 401 1555 1555 2.28
LINK O ALA A 227 CA CA A 399 1555 1555 2.31
LINK O LEU A 205 CA CA A 400 1555 1555 2.31
LINK OE1 GLU A 229 CA CA A 399 1555 1555 2.32
LINK OE1 GLN A 110 CA CA A 399 1555 1555 2.35
LINK OD1 ASP A 212 CA CA A 401 1555 1555 2.37
LINK OD2 ASP A 216 CA CA A 403 1555 1555 2.38
LINK CA CA A 399 O HOH A 420 1555 1555 2.38
LINK OD2 ASP A 225 CA CA A 401 1555 1555 2.38
LINK O ILE A 168 CA CA A 402 1555 1555 2.39
LINK OD1 ASP A 214 CA CA A 403 1555 1555 2.41
LINK OD2 ASP A 214 CA CA A 401 1555 1555 2.45
LINK OD1 ASN A 166 CA CA A 402 1555 1555 2.45
LINK OE2 GLU A 229 CA CA A 399 1555 1555 2.46
LINK CA CA A 400 O HOH A 578 1555 1555 2.48
LINK OD1 ASP A 216 CA CA A 401 1555 1555 2.52
LINK O LEU A 164 CA CA A 402 1555 1555 2.52
LINK OD1 ASP A 124 CA CA A 402 1555 1555 2.56
LINK CA CA A 399 O HOH A 413 1555 1555 2.60
LINK OD1 ASP A 222 CA CA A 403 1555 1555 2.61
LINK OD2 ASP A 224 CA CA A 403 1555 1555 2.70
LINK OD2 ASP A 124 CA CA A 402 1555 1555 2.71
LINK OD2 ASP A 222 CA CA A 403 1555 1555 2.72
CISPEP 1 TYR A 272 PRO A 273 0 2.88
CISPEP 2 PRO A 313 ASP A 314 0 -6.84
SITE 1 AC1 6 VAL A 108 GLN A 110 ALA A 227 GLU A 229
SITE 2 AC1 6 HOH A 413 HOH A 420
SITE 1 AC2 6 LEU A 205 ASP A 208 VAL A 210 ASP A 226
SITE 2 AC2 6 HOH A 406 HOH A 578
SITE 1 AC3 6 ASP A 212 ASP A 214 ASP A 216 ILE A 218
SITE 2 AC3 6 ASP A 222 ASP A 225
SITE 1 AC4 6 GLN A 84 ASP A 124 LEU A 164 ASN A 166
SITE 2 AC4 6 ILE A 168 VAL A 170
SITE 1 AC5 4 ASP A 214 ASP A 216 ASP A 222 ASP A 224
CRYST1 73.434 92.780 124.279 90.00 90.00 90.00 I 2 2 2 8
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 0.013618 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010778 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008046 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
