HEADER HYDROLASE 09-JAN-17 5MTD TITLE CRYSTAL STRUCTURE OF PDF FROM THE VIBRIO PARAHAEMOLYTICUS TITLE 2 BACTERIOPHAGE VP16T - CRYSTAL FORM II COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN ORF60T; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PHAGE VP16T; SOURCE 3 ORGANISM_TAXID: 238892; SOURCE 4 GENE: ORF60T; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PAL421TR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PBAD/MYC-HISA KEYWDS PDF, PEPTIDE DEFORMYLASE, TYPE 1B, BACTERIOPHAGE VP16T, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,R.GRZELA,C.GIGLIONE,T.MEINNEL REVDAT 2 17-JAN-24 5MTD 1 LINK REVDAT 1 20-SEP-17 5MTD 0 JRNL AUTH R.GRZELA,J.NUSBAUM,S.FIEULAINE,F.LAVECCHIA,W.V.BIENVENUT, JRNL AUTH 2 C.DIAN,T.MEINNEL,C.GIGLIONE JRNL TITL THE C-TERMINAL RESIDUE OF PHAGE VP16 PDF, THE SMALLEST JRNL TITL 2 PEPTIDE DEFORMYLASE, ACTS AS AN OFFSET ELEMENT LOCKING THE JRNL TITL 3 ACTIVE CONFORMATION. JRNL REF SCI REP V. 7 11041 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28887476 JRNL DOI 10.1038/S41598-017-11329-3 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 46328 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2439 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3344 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 176 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2049 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 329 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.16000 REMARK 3 B12 (A**2) : 0.05000 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): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.296 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2107 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2855 ; 1.311 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 272 ; 5.344 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;37.091 ;24.474 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 354 ;12.274 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;17.631 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 338 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1529 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1037 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1466 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 215 ; 0.137 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.091 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 39 ; 0.244 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.062 ; 0.200 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): 1405 ; 0.782 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2189 ; 1.182 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 788 ; 2.032 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 665 ; 2.987 ; 4.500 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 137 REMARK 3 ORIGIN FOR THE GROUP (A): -4.2145 -32.5659 16.5417 REMARK 3 T TENSOR REMARK 3 T11: -0.2137 T22: -0.2114 REMARK 3 T33: -0.2346 T12: 0.0099 REMARK 3 T13: 0.0013 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 1.7891 L22: 2.8416 REMARK 3 L33: 1.5438 L12: -0.1564 REMARK 3 L13: -0.6256 L23: 1.3542 REMARK 3 S TENSOR REMARK 3 S11: -0.0106 S12: 0.1674 S13: 0.0057 REMARK 3 S21: -0.0091 S22: -0.0732 S23: 0.1017 REMARK 3 S31: -0.0288 S32: -0.1613 S33: 0.0838 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 137 REMARK 3 ORIGIN FOR THE GROUP (A): 7.4719 -21.0115 -6.1957 REMARK 3 T TENSOR REMARK 3 T11: -0.2392 T22: -0.2067 REMARK 3 T33: -0.2101 T12: -0.0065 REMARK 3 T13: 0.0266 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 1.3883 L22: 2.0884 REMARK 3 L33: 1.7223 L12: -0.6864 REMARK 3 L13: 0.6550 L23: 0.3422 REMARK 3 S TENSOR REMARK 3 S11: 0.0466 S12: 0.0692 S13: 0.0813 REMARK 3 S21: -0.1567 S22: -0.0310 S23: 0.0034 REMARK 3 S31: -0.0439 S32: -0.1693 S33: -0.0156 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5MTD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1200002988. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980110 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48767 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.320 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 17.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.36 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58100 REMARK 200 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: PHASER REMARK 200 STARTING MODEL: 1LRY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG-1000 100MM SODIUM ACETATE, PH REMARK 280 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.79333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.89667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.89667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 83.79333 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 LYS A 2 CG CD CE NZ REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 ASP B 7 CG OD1 OD2 REMARK 470 LYS B 25 CG CD CE NZ REMARK 470 ARG B 58 CG CD 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 A 344 O HOH A 391 2.00 REMARK 500 O HOH B 390 O HOH B 393 2.03 REMARK 500 O4 PGE A 201 O HOH A 301 2.16 REMARK 500 O HOH A 347 O HOH A 456 2.19 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 CYS A 124 CA - CB - SG ANGL. DEV. = 12.8 DEGREES REMARK 500 CYS B 124 CA - CB - SG ANGL. DEV. = 9.0 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 ASP B 6 -88.46 30.90 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 NI A 203 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 1 N REMARK 620 2 MET A 1 O 79.5 REMARK 620 3 HOH A 370 O 96.4 84.4 REMARK 620 4 HOH A 373 O 164.0 85.7 88.1 REMARK 620 5 HOH A 378 O 89.6 87.6 169.0 83.7 REMARK 620 6 HIS B 74 NE2 100.6 179.1 96.5 94.1 91.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 204 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 12 NE2 REMARK 620 2 ASP B 26 OD2 112.5 REMARK 620 3 ASP B 30 OD2 108.3 4.2 REMARK 620 4 HOH B 310 O 163.4 74.0 78.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 205 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 74 NE2 REMARK 620 2 HOH A 412 O 94.4 REMARK 620 3 ASP B 76 OD1 74.9 114.2 REMARK 620 4 HOH B 324 O 91.2 80.2 37.0 REMARK 620 5 HOH B 326 O 163.0 81.3 121.9 104.2 REMARK 620 6 HOH B 360 O 88.5 92.4 149.2 172.6 75.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 85 SG REMARK 620 2 HIS A 127 NE2 118.4 REMARK 620 3 HIS A 131 NE2 103.7 104.1 REMARK 620 4 HOH A 344 O 135.6 93.4 96.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 85 SG REMARK 620 2 HIS B 127 NE2 119.0 REMARK 620 3 HIS B 131 NE2 102.4 106.9 REMARK 620 4 HOH B 305 O 131.2 95.2 99.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 202 DBREF 5MTD A 1 137 UNP Q6VT21 Q6VT21_9CAUD 1 137 DBREF 5MTD B 1 137 UNP Q6VT21 Q6VT21_9CAUD 1 137 SEQRES 1 A 137 MET LYS ILE LEU LYS ASP ASP ALA PRO GLU LEU HIS ALA SEQRES 2 A 137 ILE ALA ALA GLU VAL PRO HIS GLY GLU ASP VAL LYS ASP SEQRES 3 A 137 LEU VAL LEU ASP MET THR ALA ALA MET THR ALA ALA GLY SEQRES 4 A 137 GLY ILE GLY LEU ALA GLY ASN GLN VAL GLY VAL LEU LYS SEQRES 5 A 137 ARG ILE ILE VAL LEU ARG CYS PRO THR PHE LYS GLY CYS SEQRES 6 A 137 VAL ILE ASN PRO ILE ILE THR ARG HIS THR ASP GLY HIS SEQRES 7 A 137 VAL TYR SER PRO GLU GLY CYS LEU SER TYR PRO GLY LYS SEQRES 8 A 137 THR VAL ALA LYS LYS ARG ARG ASN LYS VAL VAL VAL GLU SEQRES 9 A 137 GLY TYR ASP MET ASP TRP GLN PRO ILE THR ILE ALA ALA SEQRES 10 A 137 LYS GLY LEU THR ALA PHE CYS LEU GLN HIS GLU ILE ASP SEQRES 11 A 137 HIS LEU ASN GLY VAL THR ILE SEQRES 1 B 137 MET LYS ILE LEU LYS ASP ASP ALA PRO GLU LEU HIS ALA SEQRES 2 B 137 ILE ALA ALA GLU VAL PRO HIS GLY GLU ASP VAL LYS ASP SEQRES 3 B 137 LEU VAL LEU ASP MET THR ALA ALA MET THR ALA ALA GLY SEQRES 4 B 137 GLY ILE GLY LEU ALA GLY ASN GLN VAL GLY VAL LEU LYS SEQRES 5 B 137 ARG ILE ILE VAL LEU ARG CYS PRO THR PHE LYS GLY CYS SEQRES 6 B 137 VAL ILE ASN PRO ILE ILE THR ARG HIS THR ASP GLY HIS SEQRES 7 B 137 VAL TYR SER PRO GLU GLY CYS LEU SER TYR PRO GLY LYS SEQRES 8 B 137 THR VAL ALA LYS LYS ARG ARG ASN LYS VAL VAL VAL GLU SEQRES 9 B 137 GLY TYR ASP MET ASP TRP GLN PRO ILE THR ILE ALA ALA SEQRES 10 B 137 LYS GLY LEU THR ALA PHE CYS LEU GLN HIS GLU ILE ASP SEQRES 11 B 137 HIS LEU ASN GLY VAL THR ILE HET PGE A 201 10 HET ZN A 202 1 HET NI A 203 1 HET NI A 204 1 HET NI A 205 1 HET PGE B 201 10 HET ZN B 202 1 HETNAM PGE TRIETHYLENE GLYCOL HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION FORMUL 3 PGE 2(C6 H14 O4) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 NI 3(NI 2+) FORMUL 10 HOH *329(H2 O) HELIX 1 AA1 ALA A 8 HIS A 12 5 5 HELIX 2 AA2 VAL A 24 ALA A 38 1 15 HELIX 3 AA3 ASN A 46 GLY A 49 5 4 HELIX 4 AA4 GLY A 119 ASN A 133 1 15 HELIX 5 AA5 ALA B 8 ALA B 13 5 6 HELIX 6 AA6 VAL B 24 ALA B 38 1 15 HELIX 7 AA7 ASN B 46 GLY B 49 5 4 HELIX 8 AA8 GLY B 119 ASN B 133 1 15 SHEET 1 AA1 5 GLY A 42 ALA A 44 0 SHEET 2 AA1 5 ILE A 54 CYS A 59 -1 O VAL A 56 N LEU A 43 SHEET 3 AA1 5 PHE A 62 HIS A 74 -1 O PHE A 62 N CYS A 59 SHEET 4 AA1 5 LYS A 100 TYR A 106 -1 O TYR A 106 N ILE A 67 SHEET 5 AA1 5 PRO A 112 LYS A 118 -1 O ILE A 115 N VAL A 103 SHEET 1 AA2 2 VAL A 79 GLU A 83 0 SHEET 2 AA2 2 VAL A 93 ARG A 97 -1 O LYS A 95 N SER A 81 SHEET 1 AA3 5 GLY B 42 ALA B 44 0 SHEET 2 AA3 5 ILE B 54 CYS B 59 -1 O VAL B 56 N LEU B 43 SHEET 3 AA3 5 PHE B 62 HIS B 74 -1 O PHE B 62 N CYS B 59 SHEET 4 AA3 5 LYS B 100 TYR B 106 -1 O TYR B 106 N ILE B 67 SHEET 5 AA3 5 PRO B 112 LYS B 118 -1 O ILE B 115 N VAL B 103 SHEET 1 AA4 2 VAL B 79 GLU B 83 0 SHEET 2 AA4 2 VAL B 93 ARG B 97 -1 O ARG B 97 N VAL B 79 SSBOND 1 CYS A 59 CYS A 124 1555 1555 2.06 SSBOND 2 CYS B 59 CYS B 124 1555 1555 2.32 LINK N MET A 1 NI NI A 203 1555 1555 2.15 LINK O MET A 1 NI NI A 203 1555 1555 2.11 LINK NE2 HIS A 12 NI NI A 204 1555 1555 2.12 LINK NE2 HIS A 74 NI NI A 205 1555 1555 2.13 LINK SG CYS A 85 ZN ZN A 202 1555 1555 2.25 LINK NE2 HIS A 127 ZN ZN A 202 1555 1555 2.04 LINK NE2 HIS A 131 ZN ZN A 202 1555 1555 2.04 LINK ZN ZN A 202 O HOH A 344 1555 1555 2.15 LINK NI NI A 203 O HOH A 370 1555 1555 2.14 LINK NI NI A 203 O HOH A 373 1555 1555 2.11 LINK NI NI A 203 O HOH A 378 1555 1555 2.06 LINK NI NI A 203 NE2 HIS B 74 1555 1555 2.11 LINK NI NI A 204 OD2 ASP B 26 2444 1555 2.19 LINK NI NI A 204 OD2 ASP B 30 2444 1555 2.01 LINK NI NI A 204 O HOH B 310 1555 3545 2.19 LINK NI NI A 205 O HOH A 412 1555 1555 2.21 LINK NI NI A 205 OD1 ASP B 76 5545 1555 2.01 LINK NI NI A 205 O HOH B 324 1555 5445 1.75 LINK NI NI A 205 O HOH B 326 1555 5445 2.17 LINK NI NI A 205 O HOH B 360 1555 5445 1.97 LINK SG CYS B 85 ZN ZN B 202 1555 1555 2.22 LINK NE2 HIS B 127 ZN ZN B 202 1555 1555 2.07 LINK NE2 HIS B 131 ZN ZN B 202 1555 1555 2.06 LINK ZN ZN B 202 O HOH B 305 1555 1555 2.10 SITE 1 AC1 8 PRO A 82 GLY A 84 LEU A 120 HIS A 127 SITE 2 AC1 8 GLU A 128 HOH A 301 HOH A 309 HOH A 317 SITE 1 AC2 6 GLN A 47 CYS A 85 HIS A 127 HIS A 131 SITE 2 AC2 6 HOH A 344 HOH A 391 SITE 1 AC3 5 MET A 1 HOH A 370 HOH A 373 HOH A 378 SITE 2 AC3 5 HIS B 74 SITE 1 AC4 4 HIS A 12 ASP B 26 ASP B 30 HOH B 310 SITE 1 AC5 6 HIS A 74 HOH A 412 ASP B 76 HOH B 324 SITE 2 AC5 6 HOH B 326 HOH B 360 SITE 1 AC6 11 ILE B 41 PRO B 82 GLU B 83 GLY B 84 SITE 2 AC6 11 LEU B 120 CYS B 124 HIS B 127 GLU B 128 SITE 3 AC6 11 HOH B 314 HOH B 317 HOH B 334 SITE 1 AC7 5 GLN B 47 CYS B 85 HIS B 127 HIS B 131 SITE 2 AC7 5 HOH B 305 CRYST1 64.260 64.260 125.690 90.00 90.00 120.00 P 32 2 1 12 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 0.015562 0.008985 0.000000 0.00000 SCALE2 0.000000 0.017969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007956 0.00000