HEADER TRANSFERASE/DNA 05-SEP-01 1JX4 TITLE CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARY COMPLEX TITLE 2 WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3'; COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*T*TP*CP*AP*TP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)- COMPND 7 3'; COMPND 8 CHAIN: T; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA POLYMERASE IV (FAMILY Y); COMPND 12 CHAIN: A; COMPND 13 EC: 2.7.7.7; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 7 ORGANISM_TAXID: 2287; SOURCE 8 GENE: DPO4; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS DNA POLYMERASE, PROTEIN-DNA COMPLEX, Y-FAMILY, TRANSFERASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.LING,F.BOUDSOCQ,R.WOODGATE,W.YANG REVDAT 4 16-OCT-24 1JX4 1 REMARK SEQADV LINK REVDAT 3 16-NOV-11 1JX4 1 VERSN HETATM REVDAT 2 24-FEB-09 1JX4 1 VERSN REVDAT 1 05-OCT-01 1JX4 0 JRNL AUTH H.LING,F.BOUDSOCQ,R.WOODGATE,W.YANG JRNL TITL CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN ACTION: A JRNL TITL 2 MECHANISM FOR ERROR-PRONE AND LESION-BYPASS REPLICATION. JRNL REF CELL(CAMBRIDGE,MASS.) V. 107 91 2001 JRNL REFN ISSN 0092-8674 JRNL PMID 11595188 JRNL DOI 10.1016/S0092-8674(01)00515-3 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 500.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 57010 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 SET) : 0.213 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1122 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.73 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3660 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 62 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.007 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2743 REMARK 3 NUCLEIC ACID ATOMS : 606 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 525 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.07000 REMARK 3 B22 (A**2) : 2.61800 REMARK 3 B33 (A**2) : 6.45800 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.943 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 MLHL: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES REMARK 3 AND PHASE PROBABILITY DISTRIBUTION REMARK 4 REMARK 4 1JX4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9832 REMARK 200 MONOCHROMATOR : SI CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57010 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.040 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 33.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.34 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : 0.55400 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 52.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 3350, 0.1 M HEPES (PH 7.0), REMARK 280 100 MM CALCIUM ACETATE, 2.5% GLYCEROL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 48.54500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.41000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.54500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.41000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, T, 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 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 A4393 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 DT T 1 REMARK 465 GLU A 342 REMARK 465 ALA A 343 REMARK 465 ILE A 344 REMARK 465 GLY A 345 REMARK 465 LEU A 346 REMARK 465 ASP A 347 REMARK 465 LYS A 348 REMARK 465 PHE A 349 REMARK 465 PHE A 350 REMARK 465 ASP A 351 REMARK 465 THR A 352 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 DA P 13 O3' REMARK 470 DT T 2 P OP1 OP2 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 DG P 5 O3' DG P 5 C3' -0.041 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 DG P 1 O5' - C5' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DG P 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA P 10 O3' - P - O5' ANGL. DEV. = -12.0 DEGREES REMARK 500 DA P 10 O3' - P - OP1 ANGL. DEV. = -14.9 DEGREES REMARK 500 DA P 10 O3' - P - OP1 ANGL. DEV. = 12.6 DEGREES REMARK 500 DA P 10 O5' - P - OP2 ANGL. DEV. = -5.5 DEGREES REMARK 500 DA P 10 C5' - C4' - O4' ANGL. DEV. = -12.1 DEGREES REMARK 500 DC T 3 C5' - C4' - C3' ANGL. DEV. = -11.7 DEGREES REMARK 500 DC T 3 C5' - C4' - O4' ANGL. DEV. = -11.5 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 TYR A 10 54.16 24.87 REMARK 500 SER A 96 140.57 -173.56 REMARK 500 SER A 145 -165.79 -161.63 REMARK 500 ASP A 277 79.04 32.22 REMARK 500 LYS A 278 -19.66 83.56 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 MG A4002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH P 17 O REMARK 620 2 HOH P 19 O 87.3 REMARK 620 3 ALA A 181 O 84.8 172.1 REMARK 620 4 ILE A 186 O 75.4 86.3 92.1 REMARK 620 5 HOH A4003 O 79.3 85.1 92.9 153.6 REMARK 620 6 HOH A4174 O 151.4 93.3 93.9 76.2 129.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A4001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 PHE A 8 O 85.3 REMARK 620 3 ASP A 105 OD2 112.2 83.1 REMARK 620 4 ADI A1014 O1A 162.5 91.6 84.4 REMARK 620 5 ADI A1014 O1B 89.5 123.7 147.8 77.9 REMARK 620 6 HOH A4017 O 84.5 154.4 79.2 104.8 79.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 4001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 4002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADI A 1014 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JXL RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH DIFFERENT SUBSTRATES DBREF 1JX4 A 1 352 UNP Q97W02 DPO42_SULSO 1 352 DBREF 1JX4 P 1 13 PDB 1JX4 1JX4 1 13 DBREF 1JX4 T 1 18 PDB 1JX4 1JX4 1 18 SEQADV 1JX4 MSE A 1 UNP Q97W02 MET 1 MODIFIED RESIDUE SEQADV 1JX4 MSE A 76 UNP Q97W02 MET 76 MODIFIED RESIDUE SEQADV 1JX4 MSE A 89 UNP Q97W02 MET 89 MODIFIED RESIDUE SEQADV 1JX4 MSE A 157 UNP Q97W02 MET 157 MODIFIED RESIDUE SEQADV 1JX4 MSE A 216 UNP Q97W02 MET 216 MODIFIED RESIDUE SEQADV 1JX4 MSE A 251 UNP Q97W02 MET 251 MODIFIED RESIDUE SEQRES 1 P 13 DG DG DG DG DG DA DA DG DG DA DC DT DA SEQRES 1 T 18 DT DT DC DA DT DT DA DG DT DC DC DT DT SEQRES 2 T 18 DC DC DC DC DC SEQRES 1 A 352 MSE ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA SEQRES 2 A 352 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 A 352 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 A 352 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 A 352 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 A 352 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MSE ARG LYS SEQRES 7 A 352 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MSE ASN LEU SEQRES 8 A 352 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 A 352 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 A 352 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 A 352 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 A 352 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 A 352 MSE ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 A 352 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 A 352 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 A 352 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 A 352 GLU PHE ASP LYS LEU LYS GLY MSE ILE GLY GLU ALA LYS SEQRES 18 A 352 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 A 352 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 A 352 ILE VAL THR MSE LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 A 352 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 A 352 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 A 352 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 A 352 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 A 352 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 A 352 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 A 352 LYS PHE ILE GLU ALA ILE GLY LEU ASP LYS PHE PHE ASP SEQRES 28 A 352 THR MODRES 1JX4 MSE A 1 MET SELENOMETHIONINE MODRES 1JX4 MSE A 76 MET SELENOMETHIONINE MODRES 1JX4 MSE A 89 MET SELENOMETHIONINE MODRES 1JX4 MSE A 157 MET SELENOMETHIONINE MODRES 1JX4 MSE A 216 MET SELENOMETHIONINE MODRES 1JX4 MSE A 251 MET SELENOMETHIONINE HET MSE A 1 16 HET MSE A 76 16 HET MSE A 89 8 HET MSE A 157 8 HET MSE A 216 16 HET MSE A 251 8 HET CA A4001 1 HET MG A4002 1 HET ADI A1014 25 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION HETNAM MG MAGNESIUM ION HETNAM ADI 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE FORMUL 3 MSE 6(C5 H11 N O2 SE) FORMUL 4 CA CA 2+ FORMUL 5 MG MG 2+ FORMUL 6 ADI C10 H15 N5 O8 P2 FORMUL 7 HOH *525(H2 O) HELIX 1 1 TYR A 10 ASN A 20 1 11 HELIX 2 2 PRO A 21 LYS A 24 5 4 HELIX 3 3 ASN A 47 LYS A 52 1 6 HELIX 4 4 PRO A 60 LEU A 68 1 9 HELIX 5 5 ARG A 77 ARG A 93 1 17 HELIX 6 6 ASP A 117 LYS A 137 1 21 HELIX 7 7 ASN A 147 LYS A 159 1 13 HELIX 8 8 ASP A 167 LEU A 178 1 12 HELIX 9 9 ASP A 179 VAL A 183 5 5 HELIX 10 10 GLY A 187 LYS A 196 1 10 HELIX 11 11 LYS A 201 SER A 207 5 7 HELIX 12 12 GLU A 209 GLY A 218 1 10 HELIX 13 13 GLY A 218 ARG A 230 1 13 HELIX 14 14 ASN A 257 ASP A 277 1 21 HELIX 15 15 SER A 307 ASP A 326 1 20 SHEET 1 A 5 ILE A 99 SER A 103 0 SHEET 2 A 5 GLU A 106 ASP A 110 -1 O TYR A 108 N GLU A 100 SHEET 3 A 5 VAL A 3 PHE A 8 -1 N LEU A 4 O LEU A 109 SHEET 4 A 5 VAL A 140 SER A 145 -1 O GLY A 143 N PHE A 5 SHEET 5 A 5 ILE A 163 VAL A 165 1 O LYS A 164 N ILE A 144 SHEET 1 B 3 GLY A 41 ALA A 46 0 SHEET 2 B 3 VAL A 28 PHE A 33 -1 N VAL A 32 O ALA A 42 SHEET 3 B 3 VAL A 72 PRO A 75 1 O LEU A 74 N CYS A 31 SHEET 1 C 4 SER A 244 SER A 255 0 SHEET 2 C 4 ILE A 330 PHE A 340 -1 O PHE A 337 N ILE A 245 SHEET 3 C 4 PRO A 281 THR A 290 -1 N VAL A 289 O ARG A 331 SHEET 4 C 4 ILE A 295 THR A 301 -1 O VAL A 296 N ALA A 288 LINK C AMSE A 1 N ILE A 2 1555 1555 1.33 LINK C BMSE A 1 N ILE A 2 1555 1555 1.32 LINK C PRO A 75 N AMSE A 76 1555 1555 1.33 LINK C PRO A 75 N BMSE A 76 1555 1555 1.32 LINK C AMSE A 76 N ARG A 77 1555 1555 1.31 LINK C BMSE A 76 N ARG A 77 1555 1555 1.33 LINK C ILE A 88 N MSE A 89 1555 1555 1.33 LINK C MSE A 89 N ASN A 90 1555 1555 1.33 LINK C ASP A 156 N MSE A 157 1555 1555 1.32 LINK C MSE A 157 N ALA A 158 1555 1555 1.32 LINK C GLY A 215 N AMSE A 216 1555 1555 1.32 LINK C GLY A 215 N BMSE A 216 1555 1555 1.32 LINK C AMSE A 216 N ILE A 217 1555 1555 1.32 LINK C BMSE A 216 N ILE A 217 1555 1555 1.35 LINK C THR A 250 N MSE A 251 1555 1555 1.33 LINK C MSE A 251 N LYS A 252 1555 1555 1.32 LINK O HOH P 17 MG MG A4002 1555 1555 2.35 LINK O HOH P 19 MG MG A4002 1555 1555 2.31 LINK OD1 ASP A 7 CA CA A4001 1555 1555 2.22 LINK O PHE A 8 CA CA A4001 1555 1555 2.28 LINK OD2 ASP A 105 CA CA A4001 1555 1555 2.23 LINK O ALA A 181 MG MG A4002 1555 1555 2.30 LINK O ILE A 186 MG MG A4002 1555 1555 2.45 LINK O1A ADI A1014 CA CA A4001 1555 1555 2.24 LINK O1B ADI A1014 CA CA A4001 1555 1555 2.30 LINK CA CA A4001 O HOH A4017 1555 1555 2.58 LINK MG MG A4002 O HOH A4003 1555 1555 1.78 LINK MG MG A4002 O HOH A4174 1555 1555 2.05 CISPEP 1 LYS A 159 PRO A 160 0 -0.24 SITE 1 AC1 5 ASP A 7 PHE A 8 ASP A 105 ADI A1014 SITE 2 AC1 5 HOH A4017 SITE 1 AC2 6 ALA A 181 ILE A 186 HOH A4003 HOH A4174 SITE 2 AC2 6 HOH P 17 HOH P 19 SITE 1 AC3 24 ASP A 7 PHE A 8 TYR A 10 PHE A 11 SITE 2 AC3 24 TYR A 12 ALA A 44 THR A 45 ARG A 51 SITE 3 AC3 24 ALA A 57 MSE A 76 ASP A 105 LYS A 159 SITE 4 AC3 24 CA A4001 HOH A4004 HOH A4074 HOH A4113 SITE 5 AC3 24 HOH A4124 HOH A4128 HOH A4159 HOH A4184 SITE 6 AC3 24 HOH A4294 DA P 13 DT T 5 DT T 6 CRYST1 97.090 102.820 52.300 90.00 90.00 90.00 P 21 21 2 4 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 0.010300 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009726 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019120 0.00000