HEADER HYDROLASE 27-FEB-13 3ZPG TITLE ACINETOBACTER BAUMANNII RIBD, FORM 2 CAVEAT 3ZPG 5GP A 1367 HAS WRONG CHIRALITY AT ATOM C4' COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBD; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.4.26, 1.1.1.193; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 ATCC: 19606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15BTEV KEYWDS REDUCTASE, DEAMINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.DAWSON,P.TRUMPER,G.CHRYSOSTOMOU,W.N.HUNTER REVDAT 4 20-DEC-23 3ZPG 1 REMARK LINK REVDAT 3 28-JUN-17 3ZPG 1 REMARK REVDAT 2 12-JUN-13 3ZPG 1 JRNL REVDAT 1 27-MAR-13 3ZPG 0 JRNL AUTH A.DAWSON,P.TRUMPER,G.CHRYSOSTOMOU,W.N.HUNTER JRNL TITL STRUCTURE OF DIAMINOHYDROXYPHOSPHORIBOSYLAMINOPYRIMIDINE JRNL TITL 2 DEAMINASE/5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL REDUCTASE JRNL TITL 3 FROM ACINETOBACTER BAUMANNII. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 69 611 2013 JRNL REFN ESSN 1744-3091 JRNL PMID 23722836 JRNL DOI 10.1107/S174430911301292X REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 36017 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1897 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) : 1.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2455 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 128 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2714 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.52000 REMARK 3 B22 (A**2) : 0.52000 REMARK 3 B33 (A**2) : -1.05000 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): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.138 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.342 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2874 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3908 ; 1.288 ; 2.011 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 356 ; 5.631 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;43.652 ;24.918 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 507 ;14.411 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;20.453 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 455 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2122 ; 0.005 ; 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): 1775 ; 0.597 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2865 ; 1.109 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1099 ; 1.770 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1041 ; 2.808 ; 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 2 A 88 REMARK 3 ORIGIN FOR THE GROUP (A): 13.5950 -14.1200 -24.5650 REMARK 3 T TENSOR REMARK 3 T11: 0.3186 T22: 0.2526 REMARK 3 T33: 0.5364 T12: -0.0778 REMARK 3 T13: 0.3081 T23: -0.0064 REMARK 3 L TENSOR REMARK 3 L11: 6.0001 L22: 4.3068 REMARK 3 L33: 1.3729 L12: 1.8534 REMARK 3 L13: -1.3706 L23: -1.1084 REMARK 3 S TENSOR REMARK 3 S11: -0.0627 S12: -0.1290 S13: -0.0524 REMARK 3 S21: -0.4601 S22: -0.0525 S23: -0.9207 REMARK 3 S31: -0.0491 S32: 0.5083 S33: 0.1152 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 : A 89 A 357 REMARK 3 ORIGIN FOR THE GROUP (A): -9.7760 -25.7200 -17.7070 REMARK 3 T TENSOR REMARK 3 T11: 0.2647 T22: 0.0300 REMARK 3 T33: 0.2273 T12: 0.0271 REMARK 3 T13: 0.1173 T23: 0.0140 REMARK 3 L TENSOR REMARK 3 L11: 0.9920 L22: 1.6806 REMARK 3 L33: 1.3184 L12: 0.0868 REMARK 3 L13: -0.0368 L23: 0.4525 REMARK 3 S TENSOR REMARK 3 S11: -0.1354 S12: -0.0137 S13: -0.1464 REMARK 3 S21: -0.4035 S22: 0.0120 S23: -0.2312 REMARK 3 S31: 0.0458 S32: 0.0895 S33: 0.1234 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 3ZPG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1290055991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38040 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 51.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 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: PDB ENTRY 3ZPC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.125 M SODIUM REMARK 280 CACODYLATE, 30% W/V POLYETHYLENE GLYCOL 8000 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 100.72800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.49900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.49900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 151.09200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.49900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.49900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.36400 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.49900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.49900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 151.09200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.49900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.49900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.36400 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 100.72800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -177.5 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LYS A 173 REMARK 465 TRP A 174 REMARK 465 GLN A 358 REMARK 465 GLU A 359 REMARK 465 LYS A 360 REMARK 465 VAL A 361 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 O2 OXL A 1363 O HOH A 2088 2.02 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 LEU A 138 CA - CB - CG ANGL. DEV. = 14.6 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 LYS A 49 148.39 -174.94 REMARK 500 ASN A 139 47.66 -146.44 REMARK 500 ASN A 244 70.24 -117.50 REMARK 500 ASP A 347 -105.05 59.47 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 A1358 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 54 ND1 REMARK 620 2 CYS A 79 SG 103.3 REMARK 620 3 CYS A 88 SG 101.6 112.0 REMARK 620 4 CAC A1364 O1 132.7 96.8 109.7 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 ZN A 1358 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1359 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP A 1361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXL A 1362 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXL A 1363 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAC A 1364 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1365 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1366 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP A 1367 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZPC RELATED DB: PDB REMARK 900 ACINETOBACTER BAUMANNII RIBD, FORM 1 DBREF 3ZPG A 1 361 UNP D0CB74 D0CB74_ACIBA 1 361 SEQADV 3ZPG MET A -20 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG GLY A -19 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG SER A -18 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG SER A -17 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG HIS A -16 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG HIS A -15 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG HIS A -14 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG HIS A -13 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG HIS A -12 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG HIS A -11 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG SER A -10 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG SER A -9 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG GLY A -8 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG GLU A -7 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG ASN A -6 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG LEU A -5 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG TYR A -4 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG PHE A -3 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG GLN A -2 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG GLY A -1 UNP D0CB74 EXPRESSION TAG SEQADV 3ZPG HIS A 0 UNP D0CB74 EXPRESSION TAG SEQRES 1 A 382 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 382 GLU ASN LEU TYR PHE GLN GLY HIS MET SER GLU LEU LYS SEQRES 3 A 382 GLN ASP GLN TYR TRP MET GLN GLN ALA ILE GLU LEU ALA SEQRES 4 A 382 LYS ARG GLY LEU TYR SER THR LYS PRO ASN PRO ASN VAL SEQRES 5 A 382 GLY CYS VAL ILE VAL LYS ASP ASP GLN LEU ILE GLY GLU SEQRES 6 A 382 GLY PHE HIS PRO LYS ALA GLY GLN PRO HIS ALA GLU VAL SEQRES 7 A 382 PHE ALA LEU ARG GLN ALA GLY GLU GLN ALA GLN GLY ALA SEQRES 8 A 382 THR ALA TYR VAL THR LEU GLU PRO CYS ALA HIS TYR GLY SEQRES 9 A 382 ARG THR PRO PRO CYS ALA GLU ALA LEU VAL LYS ALA GLN SEQRES 10 A 382 VAL LYS LYS VAL VAL VAL ALA CYS PRO ASP PRO ASN PRO SEQRES 11 A 382 LEU VAL ALA GLY LYS GLY VAL GLN ILE LEU LYS ASN ALA SEQRES 12 A 382 GLY ILE GLU VAL GLU ILE GLY ILE CYS GLU ASP LEU ALA SEQRES 13 A 382 ALA LYS LEU ASN GLN GLY PHE LEU LYS ALA MET SER THR SEQRES 14 A 382 GLY MET PRO TYR VAL ARG LEU LYS VAL ALA SER SER LEU SEQRES 15 A 382 ASP GLY ARG THR ALA MET ALA SER GLY GLU SER LYS TRP SEQRES 16 A 382 ILE THR GLY SER ALA ALA ARG GLN ASP VAL GLN HIS TRP SEQRES 17 A 382 ARG ALA ILE SER GLY ALA VAL ILE THR GLY ILE ASP THR SEQRES 18 A 382 VAL ILE ALA ASP ASP CYS GLN LEU ASN VAL ARG SER LEU SEQRES 19 A 382 HIS ASN ILE ASP ILE GLU THR VAL ALA GLN PRO LYS ARG SEQRES 20 A 382 VAL ILE LEU ASP ARG ARG GLY ARG LEU PRO LEU THR ALA SEQRES 21 A 382 LYS ILE LEU GLU ASN PRO GLU THR VAL MET VAL MET GLY SEQRES 22 A 382 PRO TYR ARG GLN GLU LEU ALA ASP LEU GLY VAL ILE GLN SEQRES 23 A 382 LEU GLU ILE GLN PRO LEU LYS THR LEU LEU GLN THR LEU SEQRES 24 A 382 SER LYS GLN TYR GLN ILE TYR ASP VAL LEU ILE GLU ALA SEQRES 25 A 382 GLY ALA THR LEU SER SER ALA PHE LEU GLN GLU GLY LEU SEQRES 26 A 382 ILE ASP GLU MET ILE SER TYR VAL ALA PRO THR LEU LEU SEQRES 27 A 382 GLY GLN SER ALA ARG ALA MET PHE ASN ALA ASP PHE GLU SEQRES 28 A 382 TYR MET ALA GLN GLN LEU ARG PHE LYS LEU LEU ASP VAL SEQRES 29 A 382 ILE GLN LEU ASP GLN ASP ILE ARG LEU ARG LEU ILE PRO SEQRES 30 A 382 THR GLN GLU LYS VAL HET ZN A1358 1 HET SO4 A1359 5 HET SO4 A1360 5 HET 5GP A1361 24 HET OXL A1362 6 HET OXL A1363 6 HET CAC A1364 5 HET CL A1365 1 HET ACT A1366 4 HET 5GP A1367 24 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE HETNAM OXL OXALATE ION HETNAM CAC CACODYLATE ION HETNAM CL CHLORIDE ION HETNAM ACT ACETATE ION HETSYN CAC DIMETHYLARSINATE FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 5GP 2(C10 H14 N5 O8 P) FORMUL 6 OXL 2(C2 O4 2-) FORMUL 8 CAC C2 H6 AS O2 1- FORMUL 9 CL CL 1- FORMUL 10 ACT C2 H3 O2 1- FORMUL 12 HOH *127(H2 O) HELIX 1 1 SER A 2 LYS A 19 1 18 HELIX 2 2 ARG A 20 LEU A 22 5 3 HELIX 3 3 HIS A 54 GLY A 64 1 11 HELIX 4 4 GLU A 65 GLN A 68 5 4 HELIX 5 5 PRO A 87 ALA A 95 1 9 HELIX 6 6 GLY A 113 ALA A 122 1 10 HELIX 7 7 CYS A 131 LYS A 137 1 7 HELIX 8 8 ASN A 139 GLY A 149 1 11 HELIX 9 9 GLY A 177 ILE A 190 1 14 HELIX 10 10 ILE A 198 ASP A 205 1 8 HELIX 11 11 ASP A 217 VAL A 221 5 5 HELIX 12 12 ALA A 239 GLU A 243 5 5 HELIX 13 13 ASN A 244 GLU A 246 5 3 HELIX 14 14 ARG A 255 LEU A 261 1 7 HELIX 15 15 PRO A 270 GLN A 283 1 14 HELIX 16 16 GLY A 292 GLU A 302 1 11 HELIX 17 17 TYR A 331 GLN A 335 5 5 SHEET 1 AA 5 GLN A 40 PHE A 46 0 SHEET 2 AA 5 GLY A 32 LYS A 37 -1 O CYS A 33 N GLY A 45 SHEET 3 AA 5 THR A 71 LEU A 76 -1 O THR A 71 N VAL A 36 SHEET 4 AA 5 LYS A 99 CYS A 104 1 O LYS A 99 N ALA A 72 SHEET 5 AA 5 GLU A 125 ILE A 128 1 O GLU A 125 N VAL A 100 SHEET 1 AB 9 ILE A 264 LEU A 266 0 SHEET 2 AB 9 VAL A 248 MET A 251 1 O VAL A 248 N ILE A 264 SHEET 3 AB 9 LYS A 225 LEU A 229 1 O ARG A 226 N MET A 249 SHEET 4 AB 9 ALA A 193 GLY A 197 1 O VAL A 194 N VAL A 227 SHEET 5 AB 9 ASP A 286 GLU A 290 1 O LEU A 288 N ILE A 195 SHEET 6 AB 9 TYR A 152 SER A 160 1 O TYR A 152 N VAL A 287 SHEET 7 AB 9 GLU A 307 ALA A 313 1 O GLU A 307 N LEU A 155 SHEET 8 AB 9 ASP A 349 PRO A 356 -1 O ILE A 350 N VAL A 312 SHEET 9 AB 9 PHE A 338 LEU A 346 -1 O LYS A 339 N ILE A 355 LINK ND1 HIS A 54 ZN ZN A1358 1555 1555 2.04 LINK SG CYS A 79 ZN ZN A1358 1555 1555 2.40 LINK SG CYS A 88 ZN ZN A1358 1555 1555 2.41 LINK ZN ZN A1358 O1 CAC A1364 1555 1555 2.01 CISPEP 1 LYS A 26 PRO A 27 0 7.28 SITE 1 AC1 4 HIS A 54 CYS A 79 CYS A 88 CAC A1364 SITE 1 AC2 5 ARG A 188 CYS A 206 GLN A 207 LEU A 208 SITE 2 AC2 5 ARG A 211 SITE 1 AC3 4 HIS A 54 GLY A 83 ARG A 84 THR A 85 SITE 1 AC4 13 LEU A 229 ARG A 231 MET A 251 PRO A 270 SITE 2 AC4 13 LEU A 271 ALA A 298 GLU A 302 HOH A2087 SITE 3 AC4 13 HOH A2101 HOH A2102 HOH A2123 HOH A2124 SITE 4 AC4 13 HOH A2125 SITE 1 AC5 4 PHE A 46 PRO A 48 PHE A 58 HOH A2126 SITE 1 AC6 6 ILE A 198 LEU A 229 ARG A 231 ARG A 232 SITE 2 AC6 6 ARG A 234 HOH A2088 SITE 1 AC7 9 HIS A 54 GLU A 56 LEU A 76 GLU A 77 SITE 2 AC7 9 PRO A 78 CYS A 79 CYS A 88 ZN A1358 SITE 3 AC7 9 HOH A2023 SITE 1 AC8 4 GLY A 197 THR A 200 GLY A 292 HOH A2107 SITE 1 AC9 6 LYS A 137 LEU A 138 ASN A 139 GLN A 140 SITE 2 AC9 6 ARG A 154 ASP A 286 SITE 1 BC1 6 LYS A 137 ASP A 183 HIS A 186 ARG A 351 SITE 2 BC1 6 ARG A 353 HOH A2127 CRYST1 72.998 72.998 201.456 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 0.013699 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004964 0.00000