HEADER HYDROLASE/HYDROLASE INHIBITOR 30-MAR-15 4Z2K
TITLE SERRATIA MARCESCENS CHITINASE B COMPLEXED WITH MACROLIDE INHIBITOR 32
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CHITINASE B;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.2.1.14;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SERRATIA MARCESCENS;
SOURCE 3 ORGANISM_TAXID: 615;
SOURCE 4 GENE: CHIB;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI DH5ALPHA;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 668369;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRCHISB
KEYWDS CHITINASE, INHIBITOR, MACROLIDE, HYDROLASE-HYDROLASE INHIBITOR
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR N.MAITA,A.SUGAWARA,T.SUNAZUKA
REVDAT 4 08-NOV-23 4Z2K 1 REMARK
REVDAT 3 19-FEB-20 4Z2K 1 SOURCE KEYWDS JRNL REMARK
REVDAT 2 08-JUL-15 4Z2K 1 JRNL
REVDAT 1 01-JUL-15 4Z2K 0
JRNL AUTH A.SUGAWARA,N.MAITA,H.GOUDA,T.YAMAMOTO,T.HIROSE,S.KIMURA,
JRNL AUTH 2 Y.SAITO,H.NAKANO,T.KASAI,H.NAKANO,K.SHIOMI,S.HIRONO,
JRNL AUTH 3 T.WATANABE,H.TANIGUCHI,S.OMURA,T.SUNAZUKA
JRNL TITL CREATION OF CUSTOMIZED BIOACTIVITY WITHIN A 14-MEMBERED
JRNL TITL 2 MACROLIDE SCAFFOLD: DESIGN, SYNTHESIS, AND BIOLOGICAL
JRNL TITL 3 EVALUATION USING A FAMILY-18 CHITINASE
JRNL REF J.MED.CHEM. V. 58 4984 2015
JRNL REFN ISSN 0022-2623
JRNL PMID 26030312
JRNL DOI 10.1021/ACS.JMEDCHEM.5B00175
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0029
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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.21
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 41069
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) : 0.169
REMARK 3 R VALUE (WORKING SET) : 0.168
REMARK 3 FREE R VALUE : 0.194
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2179
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) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2976
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2100
REMARK 3 BIN FREE R VALUE SET COUNT : 156
REMARK 3 BIN FREE R VALUE : 0.2420
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3913
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 71
REMARK 3 SOLVENT ATOMS : 240
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 23.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.09
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.04000
REMARK 3 B22 (A**2) : 0.04000
REMARK 3 B33 (A**2) : -0.09000
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): 0.164
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.847
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4094 ; 0.012 ; 0.020
REMARK 3 BOND LENGTHS OTHERS (A): 3751 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5580 ; 1.443 ; 1.954
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8596 ; 0.700 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 497 ; 7.140 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 194 ;34.611 ;24.124
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 601 ;12.692 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;14.367 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 590 ; 0.090 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4725 ; 0.012 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1009 ; 0.002 ; 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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
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 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 : 1.20
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
REMARK 4
REMARK 4 4Z2K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-15.
REMARK 100 THE DEPOSITION ID IS D_1000208432.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 30-JAN-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0-7.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PHOTON FACTORY
REMARK 200 BEAMLINE : BL-17A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43331
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 40.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 11.30
REMARK 200 R MERGE (I) : 0.12100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 10.80
REMARK 200 R MERGE FOR SHELL (I) : 0.60500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000
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: 3WD0
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 70.76
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.21
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NA PH7.0, 0.8M AMMONIUM
REMARK 280 SULFATE, 5% (V/V) GLYCEROL, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-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 98.51500
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.87000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.87000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 147.77250
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.87000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.87000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.25750
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.87000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.87000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 147.77250
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.87000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.87000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 49.25750
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 98.51500
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3550 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 38620 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL
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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 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 658 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 ASP A -3
REMARK 465 PRO A -2
REMARK 465 SER A -1
REMARK 465 SER A 0
REMARK 465 ARG A 1
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 SER A 2 OG
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 ARG A 194 NE - CZ - NH1 ANGL. DEV. = 3.6 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 ASN A 85 100.99 -163.47
REMARK 500 LEU A 177 70.68 -151.52
REMARK 500 ALA A 228 47.90 -154.65
REMARK 500 ASP A 336 114.96 -160.46
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 LEU A 498 ALA A 499 132.28
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue M6E A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3WD0 RELATED DB: PDB
REMARK 900 3WD0 CONTAINS THE SAME PROTEIN.
REMARK 900 RELATED ID: 4Z2G RELATED DB: PDB
REMARK 900 RELATED ID: 4Z2H RELATED DB: PDB
REMARK 900 RELATED ID: 4Z2I RELATED DB: PDB
REMARK 900 RELATED ID: 4Z2J RELATED DB: PDB
REMARK 900 RELATED ID: 4Z2L RELATED DB: PDB
DBREF 4Z2K A 2 499 UNP P11797 CHIB_SERMA 2 499
SEQADV 4Z2K ASP A -3 UNP P11797 EXPRESSION TAG
SEQADV 4Z2K PRO A -2 UNP P11797 EXPRESSION TAG
SEQADV 4Z2K SER A -1 UNP P11797 EXPRESSION TAG
SEQADV 4Z2K SER A 0 UNP P11797 EXPRESSION TAG
SEQADV 4Z2K ARG A 1 UNP P11797 EXPRESSION TAG
SEQRES 1 A 503 ASP PRO SER SER ARG SER THR ARG LYS ALA VAL ILE GLY
SEQRES 2 A 503 TYR TYR PHE ILE PRO THR ASN GLN ILE ASN ASN TYR THR
SEQRES 3 A 503 GLU THR ASP THR SER VAL VAL PRO PHE PRO VAL SER ASN
SEQRES 4 A 503 ILE THR PRO ALA LYS ALA LYS GLN LEU THR HIS ILE ASN
SEQRES 5 A 503 PHE SER PHE LEU ASP ILE ASN SER ASN LEU GLU CYS ALA
SEQRES 6 A 503 TRP ASP PRO ALA THR ASN ASP ALA LYS ALA ARG ASP VAL
SEQRES 7 A 503 VAL ASN ARG LEU THR ALA LEU LYS ALA HIS ASN PRO SER
SEQRES 8 A 503 LEU ARG ILE MET PHE SER ILE GLY GLY TRP TYR TYR SER
SEQRES 9 A 503 ASN ASP LEU GLY VAL SER HIS ALA ASN TYR VAL ASN ALA
SEQRES 10 A 503 VAL LYS THR PRO ALA ALA ARG THR LYS PHE ALA GLN SER
SEQRES 11 A 503 CYS VAL ARG ILE MET LYS ASP TYR GLY PHE ASP GLY VAL
SEQRES 12 A 503 ASP ILE ASP TRP GLU TYR PRO GLN ALA ALA GLU VAL ASP
SEQRES 13 A 503 GLY PHE ILE ALA ALA LEU GLN GLU ILE ARG THR LEU LEU
SEQRES 14 A 503 ASN GLN GLN THR ILE ALA ASP GLY ARG GLN ALA LEU PRO
SEQRES 15 A 503 TYR GLN LEU THR ILE ALA GLY ALA GLY GLY ALA PHE PHE
SEQRES 16 A 503 LEU SER ARG TYR TYR SER LYS LEU ALA GLN ILE VAL ALA
SEQRES 17 A 503 PRO LEU ASP TYR ILE ASN LEU MET THR TYR ASP LEU ALA
SEQRES 18 A 503 GLY PRO TRP GLU LYS ILE THR ASN HIS GLN ALA ALA LEU
SEQRES 19 A 503 PHE GLY ASP ALA ALA GLY PRO THR PHE TYR ASN ALA LEU
SEQRES 20 A 503 ARG GLU ALA ASN LEU GLY TRP SER TRP GLU GLU LEU THR
SEQRES 21 A 503 ARG ALA PHE PRO SER PRO PHE SER LEU THR VAL ASP ALA
SEQRES 22 A 503 ALA VAL GLN GLN HIS LEU MET MET GLU GLY VAL PRO SER
SEQRES 23 A 503 ALA LYS ILE VAL MET GLY VAL PRO PHE TYR GLY ARG ALA
SEQRES 24 A 503 PHE LYS GLY VAL SER GLY GLY ASN GLY GLY GLN TYR SER
SEQRES 25 A 503 SER HIS SER THR PRO GLY GLU ASP PRO TYR PRO ASN ALA
SEQRES 26 A 503 ASP TYR TRP LEU VAL GLY CYS ASP GLU CYS VAL ARG ASP
SEQRES 27 A 503 LYS ASP PRO ARG ILE ALA SER TYR ARG GLN LEU GLU GLN
SEQRES 28 A 503 MET LEU GLN GLY ASN TYR GLY TYR GLN ARG LEU TRP ASN
SEQRES 29 A 503 ASP LYS THR LYS THR PRO TYR LEU TYR HIS ALA GLN ASN
SEQRES 30 A 503 GLY LEU PHE VAL THR TYR ASP ASP ALA GLU SER PHE LYS
SEQRES 31 A 503 TYR LYS ALA LYS TYR ILE LYS GLN GLN GLN LEU GLY GLY
SEQRES 32 A 503 VAL MET PHE TRP HIS LEU GLY GLN ASP ASN ARG ASN GLY
SEQRES 33 A 503 ASP LEU LEU ALA ALA LEU ASP ARG TYR PHE ASN ALA ALA
SEQRES 34 A 503 ASP TYR ASP ASP SER GLN LEU ASP MET GLY THR GLY LEU
SEQRES 35 A 503 ARG TYR THR GLY VAL GLY PRO GLY ASN LEU PRO ILE MET
SEQRES 36 A 503 THR ALA PRO ALA TYR VAL PRO GLY THR THR TYR ALA GLN
SEQRES 37 A 503 GLY ALA LEU VAL SER TYR GLN GLY TYR VAL TRP GLN THR
SEQRES 38 A 503 LYS TRP GLY TYR ILE THR SER ALA PRO GLY SER ASP SER
SEQRES 39 A 503 ALA TRP LEU LYS VAL GLY ARG LEU ALA
HET M6E A 501 53
HET GOL A 502 6
HET GOL A 503 6
HET GOL A 504 6
HETNAM M6E (1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,17S)-3-ETHYL-2,10-
HETNAM 2 M6E DIHYDROXY-2,6,8,10,12,15,15,17-OCTAMETHYL-5-OXO-9-
HETNAM 3 M6E (PROP-2-YN-1-YLOXY)-4,14,16-
HETNAM 4 M6E TRIOXABICYCLO[11.3.1]HEPTADEC-7-YL {7-[N'-
HETNAM 5 M6E (METHYLCARBAMOYL)CARBAMIMIDAMIDO]HEPTYL}CARBAMATE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 M6E C38 H67 N5 O10
FORMUL 3 GOL 3(C3 H8 O3)
FORMUL 6 HOH *240(H2 O)
HELIX 1 AA1 PRO A 14 ASN A 20 1 7
HELIX 2 AA2 PRO A 32 ILE A 36 5 5
HELIX 3 AA3 THR A 37 LEU A 44 1 8
HELIX 4 AA4 ASN A 67 LEU A 81 1 15
HELIX 5 AA5 LYS A 82 ASN A 85 5 4
HELIX 6 AA6 GLY A 96 ASN A 101 1 6
HELIX 7 AA7 SER A 106 VAL A 114 1 9
HELIX 8 AA8 THR A 116 GLY A 135 1 20
HELIX 9 AA9 GLN A 147 ALA A 149 5 3
HELIX 10 AB1 GLU A 150 ASP A 172 1 23
HELIX 11 AB2 GLY A 188 SER A 193 1 6
HELIX 12 AB3 ARG A 194 SER A 197 5 4
HELIX 13 AB4 LYS A 198 ALA A 204 1 7
HELIX 14 AB5 ASN A 241 ALA A 246 5 6
HELIX 15 AB6 SER A 251 PHE A 259 1 9
HELIX 16 AB7 THR A 266 MET A 276 1 11
HELIX 17 AB8 PRO A 281 ALA A 283 5 3
HELIX 18 AB9 CYS A 328 ASP A 334 1 7
HELIX 19 AC1 TYR A 342 GLY A 351 1 10
HELIX 20 AC2 ASP A 381 GLN A 395 1 15
HELIX 21 AC3 HIS A 404 ASP A 408 5 5
HELIX 22 AC4 GLY A 412 ALA A 424 1 13
HELIX 23 AC5 GLY A 444 LEU A 448 5 5
SHEET 1 AA110 CYS A 60 ALA A 61 0
SHEET 2 AA110 HIS A 46 ILE A 54 -1 N ASP A 53 O ALA A 61
SHEET 3 AA110 ARG A 89 GLY A 95 1 O SER A 93 N LEU A 52
SHEET 4 AA110 GLY A 138 ASP A 142 1 O ASP A 142 N ILE A 94
SHEET 5 AA110 GLN A 180 ALA A 186 1 O GLN A 180 N VAL A 139
SHEET 6 AA110 TYR A 208 MET A 212 1 O ASN A 210 N ILE A 183
SHEET 7 AA110 ILE A 285 PRO A 290 1 O VAL A 286 N LEU A 211
SHEET 8 AA110 GLY A 399 TRP A 403 1 O GLY A 399 N MET A 287
SHEET 9 AA110 ALA A 6 PHE A 12 1 N ILE A 8 O VAL A 400
SHEET 10 AA110 HIS A 46 ILE A 54 1 O SER A 50 N TYR A 11
SHEET 1 AA2 5 ILE A 339 SER A 341 0
SHEET 2 AA2 5 TYR A 292 LYS A 297 -1 N GLY A 293 O ALA A 340
SHEET 3 AA2 5 LEU A 375 THR A 378 -1 O PHE A 376 N PHE A 296
SHEET 4 AA2 5 THR A 365 HIS A 370 -1 N HIS A 370 O LEU A 375
SHEET 5 AA2 5 TYR A 355 ASN A 360 -1 N LEU A 358 O TYR A 367
SHEET 1 AA3 4 ILE A 450 MET A 451 0
SHEET 2 AA3 4 TRP A 492 LEU A 498 1 O ARG A 497 N MET A 451
SHEET 3 AA3 4 TYR A 473 THR A 477 -1 N GLN A 476 O LEU A 493
SHEET 4 AA3 4 LEU A 467 TYR A 470 -1 N TYR A 470 O TYR A 473
SSBOND 1 CYS A 328 CYS A 331 1555 1555 2.14
CISPEP 1 SER A 50 PHE A 51 0 -0.68
CISPEP 2 GLU A 144 TYR A 145 0 7.14
CISPEP 3 SER A 261 PRO A 262 0 0.10
CISPEP 4 ASP A 316 PRO A 317 0 -7.70
CISPEP 5 TRP A 403 HIS A 404 0 -10.76
CISPEP 6 GLY A 480 TYR A 481 0 -1.66
SITE 1 AC1 11 TYR A 10 ASP A 142 GLU A 144 ILE A 170
SITE 2 AC1 11 MET A 212 TYR A 214 ASP A 215 TRP A 220
SITE 3 AC1 11 ASP A 316 THR A 461 THR A 483
SITE 1 AC2 6 ARG A 162 ALA A 204 PRO A 205 ASP A 207
SITE 2 AC2 6 LYS A 284 HOH A 758
SITE 1 AC3 8 PRO A 260 PHE A 263 SER A 264 ARG A 439
SITE 2 AC3 8 TYR A 440 THR A 441 HOH A 651 HOH A 661
SITE 1 AC4 5 ARG A 244 PHE A 259 PRO A 260 SER A 261
SITE 2 AC4 5 HOH A 736
CRYST1 97.740 97.740 197.030 90.00 90.00 90.00 P 43 21 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 0.010231 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010231 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005075 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
