HEADER HYDROLASE 27-OCT-14 4RNZ TITLE STRUCTURE OF HELICOBACTER PYLORI CSD3 FROM THE HEXAGONAL CRYSTAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL SECRETED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 42-403; COMPND 5 SYNONYM: CSD3 CELL-SHAPE DETERMINANT; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 STRAIN: ATCC 700392 / 26695; SOURCE 5 GENE: C694_02600, HP_0506; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS M23B METALLOPEPTIDASE, METALLOPEPTIDASE, PEPTIDOGLYCAN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.R.AN,H.S.KIM,J.KIM,H.N.IM,H.J.YOON,J.Y.YOON,J.Y.JANG,D.HESEK,M.LEE, AUTHOR 2 S.MOBASHERY,S.-J.KIM,B.I.LEE,S.W.SUH REVDAT 3 28-FEB-24 4RNZ 1 REMARK SEQADV LINK REVDAT 2 25-MAR-15 4RNZ 1 JRNL REVDAT 1 11-MAR-15 4RNZ 0 JRNL AUTH D.R.AN,H.S.KIM,J.KIM,H.N.IM,H.J.YOON,J.Y.YOON,J.Y.JANG, JRNL AUTH 2 D.HESEK,M.LEE,S.MOBASHERY,S.J.KIM,B.I.LEE,S.W.SUH JRNL TITL STRUCTURE OF CSD3 FROM HELICOBACTER PYLORI, A CELL JRNL TITL 2 SHAPE-DETERMINING METALLOPEPTIDASE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 675 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 25760614 JRNL DOI 10.1107/S1399004715000152 REMARK 2 REMARK 2 RESOLUTION. 1.98 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31293 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1672 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2262 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2919 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.96000 REMARK 3 B22 (A**2) : 0.96000 REMARK 3 B33 (A**2) : -3.13000 REMARK 3 B12 (A**2) : 0.48000 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): 0.170 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.905 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3017 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2917 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4058 ; 1.420 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6705 ; 0.736 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 356 ; 6.051 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;30.162 ;23.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 542 ;13.984 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;17.912 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 433 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3336 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 737 ; 0.001 ; 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): 1433 ; 2.398 ; 3.775 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1432 ; 2.392 ; 3.773 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1786 ; 3.522 ; 5.639 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1787 ; 3.521 ; 5.641 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1584 ; 2.938 ; 4.240 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1584 ; 2.938 ; 4.240 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2273 ; 4.690 ; 6.178 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3440 ; 6.683 ;30.747 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3440 ; 6.683 ;30.746 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 4RNZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000087580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : HYBRID-TYPE OF IMAGE PLATES AND REMARK 200 A CCD REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31293 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 41.9170 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 0.87700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.519 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM DI-AMMONIUM HYDROGEN PHOSPHATE, REMARK 280 PH 7.9, 20% (V/V) PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 124.64200 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 62.32100 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 93.48150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.16050 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 155.80250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 124.64200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 62.32100 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 31.16050 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 93.48150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 155.80250 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 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 PRO A 251 REMARK 465 VAL A 252 REMARK 465 LEU A 253 REMARK 465 LYS A 254 REMARK 465 VAL A 255 REMARK 465 ARG A 256 REMARK 465 GLY A 333 REMARK 465 LEU A 334 REMARK 465 SER A 335 REMARK 465 THR A 336 REMARK 465 HIS A 410 REMARK 465 HIS A 411 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 301 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 301 NE - CZ - NH2 ANGL. DEV. = -4.5 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 A 47 -80.43 -115.74 REMARK 500 ASN A 82 -2.74 70.42 REMARK 500 ASN A 92 4.92 -69.46 REMARK 500 THR A 139 -83.81 -115.73 REMARK 500 VAL A 187 58.75 31.62 REMARK 500 SER A 205 -4.30 63.07 REMARK 500 SER A 242 114.24 -162.19 REMARK 500 TYR A 260 44.64 -94.72 REMARK 500 ASN A 298 -126.46 50.11 REMARK 500 HIS A 306 32.49 75.99 REMARK 500 LYS A 316 131.62 -37.72 REMARK 500 SER A 348 -10.64 84.20 REMARK 500 PHE A 403 -66.04 -133.27 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 74 OE2 REMARK 620 2 HIS A 259 NE2 106.7 REMARK 620 3 ASP A 263 OD1 135.8 101.1 REMARK 620 4 HIS A 341 ND1 94.2 116.6 103.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 502 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 390 NE2 REMARK 620 2 HIS A 406 NE2 113.5 REMARK 620 3 HIS A 408 NE2 97.4 118.3 REMARK 620 4 PO4 A 504 O1 106.8 96.0 125.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 503 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 407 NE2 REMARK 620 2 HIS A 409 NE2 108.5 REMARK 620 3 PO4 A 505 O4 106.4 103.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 509 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RNY RELATED DB: PDB DBREF 4RNZ A 42 403 UNP O25247 O25247_HELPY 42 403 SEQADV 4RNZ MET A 41 UNP O25247 INITIATING METHIONINE SEQADV 4RNZ LEU A 404 UNP O25247 EXPRESSION TAG SEQADV 4RNZ GLU A 405 UNP O25247 EXPRESSION TAG SEQADV 4RNZ HIS A 406 UNP O25247 EXPRESSION TAG SEQADV 4RNZ HIS A 407 UNP O25247 EXPRESSION TAG SEQADV 4RNZ HIS A 408 UNP O25247 EXPRESSION TAG SEQADV 4RNZ HIS A 409 UNP O25247 EXPRESSION TAG SEQADV 4RNZ HIS A 410 UNP O25247 EXPRESSION TAG SEQADV 4RNZ HIS A 411 UNP O25247 EXPRESSION TAG SEQRES 1 A 371 MET GLU ARG LEU VAL TRP ASP LYS LEU THR LEU LEU GLY SEQRES 2 A 371 PHE LEU GLU LYS ASN HIS ILE PRO GLN LYS LEU TYR TYR SEQRES 3 A 371 ASN LEU SER SER GLN ASP LYS GLU LEU SER ALA GLU ILE SEQRES 4 A 371 GLN SER ASN VAL THR TYR TYR THR LEU ARG ASP ALA ASN SEQRES 5 A 371 ASN THR LEU ILE GLN ALA LEU ILE PRO ILE SER GLN ASP SEQRES 6 A 371 LEU GLN ILE HIS ILE TYR LYS LYS GLY GLU ASP TYR PHE SEQRES 7 A 371 LEU ASP PHE ILE PRO ILE ILE PHE THR ARG LYS GLU LYS SEQRES 8 A 371 THR LEU LEU LEU SER LEU GLN THR SER PRO TYR GLN ASP SEQRES 9 A 371 ILE ILE LYS ALA THR ASN ASP PRO LEU LEU ALA ASN GLN SEQRES 10 A 371 LEU MET ASN ALA TYR LYS LYS SER VAL PRO PHE LYS ARG SEQRES 11 A 371 LEU VAL LYS ASN ASP LYS ILE ALA ILE VAL TYR THR ARG SEQRES 12 A 371 ASP TYR ARG VAL GLY GLN ALA PHE GLY GLN PRO THR ILE SEQRES 13 A 371 LYS MET ALA MET VAL SER SER ARG SER ASN GLN TYR TYR SEQRES 14 A 371 LEU PHE SER HIS SER ASN GLY HIS TYR TYR ASP SER LYS SEQRES 15 A 371 ALA GLN GLU VAL ALA GLY PHE LEU LEU GLU THR PRO VAL SEQRES 16 A 371 LYS TYR THR ARG ILE SER SER PRO PHE SER TYR GLY ARG SEQRES 17 A 371 PHE HIS PRO VAL LEU LYS VAL ARG ARG PRO HIS TYR GLY SEQRES 18 A 371 VAL ASP TYR ALA ALA LYS HIS GLY SER LEU ILE HIS SER SEQRES 19 A 371 ALA SER ASP GLY ARG VAL GLY PHE MET GLY VAL LYS ALA SEQRES 20 A 371 GLY TYR GLY LYS VAL VAL GLU ILE HIS LEU ASN GLU LEU SEQRES 21 A 371 ARG LEU VAL TYR ALA HIS MET SER ALA PHE ALA ASN GLY SEQRES 22 A 371 LEU LYS LYS GLY SER PHE VAL LYS LYS GLY GLN ILE ILE SEQRES 23 A 371 GLY ARG VAL GLY SER THR GLY LEU SER THR GLY PRO HIS SEQRES 24 A 371 LEU HIS PHE GLY VAL TYR LYS ASN SER ARG PRO ILE ASN SEQRES 25 A 371 PRO LEU GLY TYR ILE ARG THR ALA LYS SER LYS LEU HIS SEQRES 26 A 371 GLY LYS GLN ARG GLU VAL PHE LEU GLU LYS ALA GLN ARG SEQRES 27 A 371 SER LYS GLN LYS LEU GLU GLU LEU LEU LYS THR HIS SER SEQRES 28 A 371 PHE GLU LYS ASN SER PHE TYR LEU LEU GLU GLY PHE LEU SEQRES 29 A 371 GLU HIS HIS HIS HIS HIS HIS HET ZN A 501 1 HET NI A 502 1 HET NI A 503 1 HET PO4 A 504 5 HET PO4 A 505 5 HET PO4 A 506 5 HET GOL A 507 6 HET GOL A 508 6 HET GOL A 509 6 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 NI 2(NI 2+) FORMUL 5 PO4 3(O4 P 3-) FORMUL 8 GOL 3(C3 H8 O3) FORMUL 11 HOH *148(H2 O) HELIX 1 1 THR A 50 ASN A 58 1 9 HELIX 2 2 GLN A 62 ASN A 67 1 6 HELIX 3 3 SER A 69 ALA A 77 1 9 HELIX 4 4 SER A 140 ASN A 150 1 11 HELIX 5 5 ASP A 151 TYR A 162 1 12 HELIX 6 6 SER A 165 ARG A 170 1 6 HELIX 7 7 ASN A 352 ILE A 357 5 6 HELIX 8 8 HIS A 365 THR A 389 1 25 SHEET 1 A 5 GLU A 42 VAL A 45 0 SHEET 2 A 5 THR A 84 ARG A 89 -1 O THR A 87 N GLU A 42 SHEET 3 A 5 LEU A 95 PRO A 101 -1 O ILE A 96 N LEU A 88 SHEET 4 A 5 LEU A 106 LYS A 113 -1 O ILE A 108 N ILE A 100 SHEET 5 A 5 ASP A 116 PRO A 123 -1 O ASP A 116 N LYS A 113 SHEET 1 B 7 GLU A 225 VAL A 226 0 SHEET 2 B 7 TYR A 218 TYR A 219 -1 N TYR A 218 O VAL A 226 SHEET 3 B 7 ASN A 206 SER A 212 -1 N PHE A 211 O TYR A 219 SHEET 4 B 7 GLN A 189 SER A 203 -1 N VAL A 201 O TYR A 208 SHEET 5 B 7 LYS A 176 ARG A 186 -1 N VAL A 180 O MET A 198 SHEET 6 B 7 THR A 127 SER A 136 -1 N THR A 127 O TYR A 185 SHEET 7 B 7 PHE A 397 GLU A 401 -1 O TYR A 398 N LEU A 134 SHEET 1 C 7 ARG A 239 SER A 242 0 SHEET 2 C 7 VAL A 262 ALA A 265 -1 O ASP A 263 N SER A 242 SHEET 3 C 7 HIS A 339 LYS A 346 -1 O PHE A 342 N VAL A 262 SHEET 4 C 7 LEU A 300 PHE A 310 -1 N VAL A 303 O GLY A 343 SHEET 5 C 7 GLY A 290 LEU A 297 -1 N ILE A 295 O LEU A 302 SHEET 6 C 7 GLY A 278 LYS A 286 -1 N GLY A 284 O VAL A 292 SHEET 7 C 7 PHE A 319 VAL A 320 -1 O VAL A 320 N GLY A 278 SHEET 1 D 5 LEU A 271 HIS A 273 0 SHEET 2 D 5 ILE A 325 VAL A 329 -1 O ILE A 326 N ILE A 272 SHEET 3 D 5 LEU A 300 PHE A 310 -1 N SER A 308 O ARG A 328 SHEET 4 D 5 HIS A 339 LYS A 346 -1 O GLY A 343 N VAL A 303 SHEET 5 D 5 ARG A 349 ILE A 351 -1 O ARG A 349 N LYS A 346 LINK OE2 GLU A 74 ZN ZN A 501 1555 1555 2.00 LINK NE2 HIS A 259 ZN ZN A 501 1555 1555 1.98 LINK OD1 ASP A 263 ZN ZN A 501 1555 1555 1.97 LINK ND1 HIS A 341 ZN ZN A 501 1555 1555 2.02 LINK NE2 HIS A 390 NI NI A 502 1555 1555 2.18 LINK NE2 HIS A 406 NI NI A 502 1555 1555 2.10 LINK NE2 HIS A 407 NI NI A 503 1555 1555 2.18 LINK NE2 HIS A 408 NI NI A 502 1555 1555 1.97 LINK NE2 HIS A 409 NI NI A 503 1555 1555 1.94 LINK NI NI A 502 O1 PO4 A 504 1555 1555 2.20 LINK NI NI A 503 O4 PO4 A 505 1555 1555 2.44 SITE 1 AC1 4 GLU A 74 HIS A 259 ASP A 263 HIS A 341 SITE 1 AC2 4 HIS A 390 HIS A 406 HIS A 408 PO4 A 504 SITE 1 AC3 4 HIS A 365 HIS A 407 HIS A 409 PO4 A 505 SITE 1 AC4 5 HIS A 390 LEU A 400 HIS A 406 NI A 502 SITE 2 AC4 5 HOH A 697 SITE 1 AC5 6 HIS A 365 GLY A 366 HIS A 407 HIS A 409 SITE 2 AC5 6 NI A 503 HOH A 676 SITE 1 AC6 4 LYS A 129 LYS A 131 TYR A 185 GOL A 508 SITE 1 AC7 6 ILE A 125 ARG A 186 HIS A 273 HOH A 621 SITE 2 AC7 6 HOH A 694 HOH A 695 SITE 1 AC8 4 THR A 149 ARG A 183 PO4 A 506 GOL A 509 SITE 1 AC9 9 LEU A 153 ARG A 183 ALA A 190 PHE A 191 SITE 2 AC9 9 GLY A 192 GLN A 193 PRO A 194 GOL A 508 SITE 3 AC9 9 HOH A 747 CRYST1 91.469 91.469 186.963 90.00 90.00 120.00 P 65 2 2 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 0.010933 0.006312 0.000000 0.00000 SCALE2 0.000000 0.012624 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005349 0.00000