HEADER ADP-RIBOSE-BINDING PROTEIN 14-SEP-16 5LW0 TITLE ORYZA SATIVA APL MACRODOMAIN IN COMPLEX WITH ADP-RIBOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC HELIX-LOOP-HELIX, PUTATIVE, EXPRESSED; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 78-296; COMPND 5 SYNONYM: APL; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA SUBSP. JAPONICA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: LOC_OS03G18210; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ADP-RIBOSYLTRANSFERASE, INTERSTRAND CROSSLINK REPAIR, ADP-RIBOSE- KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.ARIZA REVDAT 3 17-JAN-24 5LW0 1 HETSYN REVDAT 2 13-SEP-17 5LW0 1 ATOM REVDAT 1 26-OCT-16 5LW0 0 JRNL AUTH A.R.GUNN,B.BANOS-PINERO,P.PASCHKE,L.SANCHEZ-PULIDO,A.ARIZA, JRNL AUTH 2 J.DAY,M.EMRICH,D.LEYS,C.P.PONTING,I.AHEL,N.D.LAKIN JRNL TITL THE ROLE OF ADP-RIBOSYLATION IN REGULATING DNA INTERSTRAND JRNL TITL 2 CROSSLINK REPAIR. JRNL REF J.CELL.SCI. V. 129 3845 2016 JRNL REFN ESSN 1477-9137 JRNL PMID 27587838 JRNL DOI 10.1242/JCS.193375 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0071 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 44846 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2344 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2734 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.2220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3113 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 97 REMARK 3 SOLVENT ATOMS : 365 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.37000 REMARK 3 B22 (A**2) : 0.14000 REMARK 3 B33 (A**2) : 0.97000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.31000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.091 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.788 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3373 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3248 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4613 ; 1.564 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7497 ; 0.958 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 440 ; 5.965 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;34.801 ;23.916 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 575 ;14.553 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;19.214 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 538 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3800 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 761 ; 0.005 ; 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): 1666 ; 2.319 ; 2.075 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1659 ; 2.277 ; 2.060 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2085 ; 3.355 ; 3.093 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2082 ; 3.357 ; 3.085 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1707 ; 3.957 ; 2.584 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1707 ; 3.957 ; 2.584 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2510 ; 5.939 ; 3.676 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4173 ; 7.940 ;18.850 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3994 ; 7.871 ;18.298 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 29 229 B 29 229 12699 0.10 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5LW0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001448. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47191 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 56.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.40600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: 5LW6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 1500 + 0.1 M SPG BUFFER REMARK 280 (SUCCINIC ACID, SODIUM PHOSPHATE MONOBASIC MONOHYDRATE AND REMARK 280 GLYCINE), PH 4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 36.74800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.65900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.74800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.65900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 B 589 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 590 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 592 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 MET A 66 REMARK 465 GLY A 67 REMARK 465 HIS A 68 REMARK 465 HIS A 69 REMARK 465 HIS A 70 REMARK 465 HIS A 71 REMARK 465 HIS A 72 REMARK 465 HIS A 73 REMARK 465 GLY A 74 REMARK 465 GLY A 75 REMARK 465 VAL A 76 REMARK 465 LYS A 77 REMARK 465 LYS A 78 REMARK 465 GLU A 79 REMARK 465 LEU A 80 REMARK 465 SER A 81 REMARK 465 ASN A 82 REMARK 465 SER A 83 REMARK 465 LYS A 84 REMARK 465 LYS A 85 REMARK 465 ILE A 86 REMARK 465 GLU A 87 REMARK 465 ASP A 88 REMARK 465 GLN A 89 REMARK 465 SER A 90 REMARK 465 ARG A 91 REMARK 465 GLU A 92 REMARK 465 SER A 93 REMARK 465 VAL A 94 REMARK 465 MET B 66 REMARK 465 GLY B 67 REMARK 465 HIS B 68 REMARK 465 HIS B 69 REMARK 465 HIS B 70 REMARK 465 HIS B 71 REMARK 465 HIS B 72 REMARK 465 HIS B 73 REMARK 465 GLY B 74 REMARK 465 GLY B 75 REMARK 465 VAL B 76 REMARK 465 LYS B 77 REMARK 465 LYS B 78 REMARK 465 GLU B 79 REMARK 465 LEU B 80 REMARK 465 SER B 81 REMARK 465 ASN B 82 REMARK 465 SER B 83 REMARK 465 LYS B 84 REMARK 465 LYS B 85 REMARK 465 ILE B 86 REMARK 465 GLU B 87 REMARK 465 ASP B 88 REMARK 465 GLN B 89 REMARK 465 SER B 90 REMARK 465 ARG B 91 REMARK 465 GLU B 92 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 OE1 GLN B 114 O HOH B 401 1.96 REMARK 500 NH2 ARG B 139 O HOH B 402 2.00 REMARK 500 OE2 GLU A 289 O HOH A 401 2.05 REMARK 500 N ASN A 137 O HOH A 402 2.06 REMARK 500 OD2 ASP A 118 O HOH A 403 2.07 REMARK 500 OD1 ASP A 226 O HOH A 404 2.11 REMARK 500 OD1 ASP A 226 O HOH A 405 2.15 REMARK 500 OD2 ASP A 126 O4 PO4 A 303 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 135 CB TYR A 135 CG 0.097 REMARK 500 TYR A 135 CD1 TYR A 135 CE1 0.104 REMARK 500 TYR A 135 CZ TYR A 135 OH 0.127 REMARK 500 CYS A 187 CA CYS A 187 CB -0.079 REMARK 500 CYS A 187 CB CYS A 187 SG -0.144 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 ARG A 168 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 MET A 261 CG - SD - CE ANGL. DEV. = -16.1 DEGREES REMARK 500 ARG B 168 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 MET B 261 CG - SD - CE ANGL. DEV. = -11.0 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 SER A 109 -5.31 81.40 REMARK 500 ALA A 111 -87.33 -116.37 REMARK 500 SER B 109 -1.66 78.22 REMARK 500 ALA B 111 -89.50 -116.85 REMARK 500 ASP B 226 -70.17 -109.62 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 AR6 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AR6 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLY B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLY B 304 DBREF 5LW0 A 78 296 UNP Q10MW4 Q10MW4_ORYSJ 78 296 DBREF 5LW0 B 78 296 UNP Q10MW4 Q10MW4_ORYSJ 78 296 SEQADV 5LW0 MET A 66 UNP Q10MW4 INITIATING METHIONINE SEQADV 5LW0 GLY A 67 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS A 68 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS A 69 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS A 70 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS A 71 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS A 72 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS A 73 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 GLY A 74 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 GLY A 75 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 VAL A 76 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 LYS A 77 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 MET B 66 UNP Q10MW4 INITIATING METHIONINE SEQADV 5LW0 GLY B 67 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS B 68 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS B 69 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS B 70 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS B 71 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS B 72 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 HIS B 73 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 GLY B 74 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 GLY B 75 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 VAL B 76 UNP Q10MW4 EXPRESSION TAG SEQADV 5LW0 LYS B 77 UNP Q10MW4 EXPRESSION TAG SEQRES 1 A 231 MET GLY HIS HIS HIS HIS HIS HIS GLY GLY VAL LYS LYS SEQRES 2 A 231 GLU LEU SER ASN SER LYS LYS ILE GLU ASP GLN SER ARG SEQRES 3 A 231 GLU SER VAL LEU SER ASP ILE SER SER ARG THR LEU ALA SEQRES 4 A 231 PHE PRO SER ILE SER THR ALA ASP PHE GLN PHE ASP LEU SEQRES 5 A 231 ASP ARG ALA SER ASP ILE ILE VAL ASP ALA VAL ALA ASP SEQRES 6 A 231 ILE LEU GLN LYS TYR ASP ASN ILE ARG LEU VAL LEU VAL SEQRES 7 A 231 ASP LEU SER HIS LYS SER ARG ILE LEU SER LEU VAL LYS SEQRES 8 A 231 GLU LYS ALA ALA LYS LYS ASN ILE ASN SER SER ARG PHE SEQRES 9 A 231 PHE THR PHE VAL GLY ASP ILE THR GLN LEU GLN SER LYS SEQRES 10 A 231 GLY GLY LEU ARG CYS ASN VAL ILE ALA ASN ALA ALA ASN SEQRES 11 A 231 TRP ARG LEU LYS PRO GLY GLY GLY GLY VAL ASN ALA ALA SEQRES 12 A 231 ILE TYR ASN ALA ALA GLY GLU ASP LEU GLN ARG ALA THR SEQRES 13 A 231 LYS GLU CYS ALA ASP THR LEU ARG PRO GLY SER SER VAL SEQRES 14 A 231 ALA VAL PRO LEU PRO SER THR SER PRO LEU HIS GLN ARG SEQRES 15 A 231 GLU GLY VAL THR HIS ILE ILE HIS VAL LEU GLY PRO ASN SEQRES 16 A 231 MET ASN PRO MET ARG PRO ASP CYS LEU LYS ASN ASP TYR SEQRES 17 A 231 THR LYS GLY SER LYS ILE LEU HIS GLU ALA TYR THR SER SEQRES 18 A 231 LEU PHE GLU ASN PHE VAL ALA ILE VAL GLN SEQRES 1 B 231 MET GLY HIS HIS HIS HIS HIS HIS GLY GLY VAL LYS LYS SEQRES 2 B 231 GLU LEU SER ASN SER LYS LYS ILE GLU ASP GLN SER ARG SEQRES 3 B 231 GLU SER VAL LEU SER ASP ILE SER SER ARG THR LEU ALA SEQRES 4 B 231 PHE PRO SER ILE SER THR ALA ASP PHE GLN PHE ASP LEU SEQRES 5 B 231 ASP ARG ALA SER ASP ILE ILE VAL ASP ALA VAL ALA ASP SEQRES 6 B 231 ILE LEU GLN LYS TYR ASP ASN ILE ARG LEU VAL LEU VAL SEQRES 7 B 231 ASP LEU SER HIS LYS SER ARG ILE LEU SER LEU VAL LYS SEQRES 8 B 231 GLU LYS ALA ALA LYS LYS ASN ILE ASN SER SER ARG PHE SEQRES 9 B 231 PHE THR PHE VAL GLY ASP ILE THR GLN LEU GLN SER LYS SEQRES 10 B 231 GLY GLY LEU ARG CYS ASN VAL ILE ALA ASN ALA ALA ASN SEQRES 11 B 231 TRP ARG LEU LYS PRO GLY GLY GLY GLY VAL ASN ALA ALA SEQRES 12 B 231 ILE TYR ASN ALA ALA GLY GLU ASP LEU GLN ARG ALA THR SEQRES 13 B 231 LYS GLU CYS ALA ASP THR LEU ARG PRO GLY SER SER VAL SEQRES 14 B 231 ALA VAL PRO LEU PRO SER THR SER PRO LEU HIS GLN ARG SEQRES 15 B 231 GLU GLY VAL THR HIS ILE ILE HIS VAL LEU GLY PRO ASN SEQRES 16 B 231 MET ASN PRO MET ARG PRO ASP CYS LEU LYS ASN ASP TYR SEQRES 17 B 231 THR LYS GLY SER LYS ILE LEU HIS GLU ALA TYR THR SER SEQRES 18 B 231 LEU PHE GLU ASN PHE VAL ALA ILE VAL GLN HET AR6 A 301 36 HET PO4 A 302 5 HET PO4 A 303 5 HET AR6 B 301 36 HET PO4 B 302 5 HET GLY B 303 5 HET GLY B 304 5 HETNAM AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY- HETNAM 2 AR6 OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5- HETNAM 3 AR6 TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN HETNAM 4 AR6 PHOSPHATE HETNAM PO4 PHOSPHATE ION HETNAM GLY GLYCINE HETSYN AR6 ADENOSINE-5-DIPHOSPHORIBOSE FORMUL 3 AR6 2(C15 H23 N5 O14 P2) FORMUL 4 PO4 3(O4 P 3-) FORMUL 8 GLY 2(C2 H5 N O2) FORMUL 10 HOH *365(H2 O) HELIX 1 AA1 ASP A 97 SER A 100 5 4 HELIX 2 AA2 ASP A 116 TYR A 135 1 20 HELIX 3 AA3 SER A 149 LYS A 162 1 14 HELIX 4 AA4 GLY A 203 GLY A 214 1 12 HELIX 5 AA5 GLY A 214 ALA A 225 1 12 HELIX 6 AA6 SER A 242 GLY A 249 1 8 HELIX 7 AA7 ASP A 272 GLN A 296 1 25 HELIX 8 AA8 ASP B 97 SER B 100 5 4 HELIX 9 AA9 ASP B 116 TYR B 135 1 20 HELIX 10 AB1 SER B 149 LYS B 162 1 14 HELIX 11 AB2 GLY B 203 GLY B 214 1 12 HELIX 12 AB3 GLY B 214 ALA B 225 1 12 HELIX 13 AB4 SER B 242 GLY B 249 1 8 HELIX 14 AB5 ASP B 272 GLN B 296 1 25 SHEET 1 AA1 6 PHE A 169 VAL A 173 0 SHEET 2 AA1 6 ARG A 139 ASP A 144 1 N LEU A 142 O PHE A 172 SHEET 3 AA1 6 THR A 102 PHE A 105 1 N LEU A 103 O VAL A 141 SHEET 4 AA1 6 VAL A 189 ALA A 193 1 O ALA A 191 N ALA A 104 SHEET 5 AA1 6 HIS A 252 LEU A 257 1 O VAL A 256 N ASN A 192 SHEET 6 AA1 6 SER A 232 PRO A 237 -1 N VAL A 236 O ILE A 253 SHEET 1 AA2 6 PHE B 169 VAL B 173 0 SHEET 2 AA2 6 ARG B 139 ASP B 144 1 N LEU B 142 O PHE B 172 SHEET 3 AA2 6 THR B 102 PHE B 105 1 N PHE B 105 O VAL B 141 SHEET 4 AA2 6 VAL B 189 ALA B 193 1 O VAL B 189 N ALA B 104 SHEET 5 AA2 6 HIS B 252 VAL B 256 1 O VAL B 256 N ASN B 192 SHEET 6 AA2 6 SER B 233 PRO B 237 -1 N VAL B 236 O ILE B 253 SITE 1 AC1 27 PRO A 106 SER A 107 SER A 109 THR A 110 SITE 2 AC1 27 ALA A 111 ASP A 112 PHE A 113 ASP A 144 SITE 3 AC1 27 LEU A 145 GLY A 174 ASP A 175 ILE A 176 SITE 4 AC1 27 ALA A 193 ALA A 194 ASN A 195 GLY A 202 SITE 5 AC1 27 GLY A 203 GLY A 204 VAL A 205 ARG A 265 SITE 6 AC1 27 HOH A 425 HOH A 431 HOH A 449 HOH A 465 SITE 7 AC1 27 HOH A 469 HOH A 477 HOH A 519 SITE 1 AC2 7 ASP A 130 THR A 285 HOH A 423 HOH A 428 SITE 2 AC2 7 HOH A 460 HOH A 535 HOH A 538 SITE 1 AC3 5 ASP A 126 HIS A 281 HOH A 419 HOH A 420 SITE 2 AC3 5 HOH A 433 SITE 1 AC4 28 PRO B 106 SER B 107 SER B 109 THR B 110 SITE 2 AC4 28 ALA B 111 ASP B 112 PHE B 113 ASP B 144 SITE 3 AC4 28 LEU B 145 GLY B 174 ASP B 175 ILE B 176 SITE 4 AC4 28 ALA B 193 ASN B 195 GLY B 201 GLY B 202 SITE 5 AC4 28 GLY B 203 GLY B 204 VAL B 205 ALA B 208 SITE 6 AC4 28 ARG B 265 HOH B 410 HOH B 424 HOH B 450 SITE 7 AC4 28 HOH B 462 HOH B 490 HOH B 491 HOH B 559 SITE 1 AC5 4 ARG B 119 ILE B 123 ASP B 126 HIS B 281 SITE 1 AC6 4 MET A 264 ASN B 165 ARG B 168 HOH B 508 SITE 1 AC7 3 GLN B 114 ASN B 262 MET B 264 CRYST1 73.496 91.318 62.882 90.00 103.32 90.00 C 1 2 1 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 0.013606 0.000000 0.003221 0.00000 SCALE2 0.000000 0.010951 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016342 0.00000