PDB Short entry for 1K3X HEADER HYDROLASE/DNA 04-OCT-01 1K3X TITLE CRYSTAL STRUCTURE OF A TRAPPED REACTION INTERMEDIATE OF THE DNA REPAIR TITLE 2 ENZYME ENDONUCLEASE VIII WITH BROMINATED-DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU) COMPND 3 P*GP*G)-3'; COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: ENDONUCLEASE VIII; COMPND 12 CHAIN: A; COMPND 13 EC: 3.2.2.-; 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: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562; SOURCE 8 GENE: NEI; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HYDROLASE/DNA, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.GOLAN,D.O.ZHARKOV,R.GILBOA,A.S.FERNANDES,J.H.KYCIA,S.E.GERCHMAN, AUTHOR 2 R.A.RIEGER,A.P.GROLLMAN,G.SHOHAM REVDAT 4 16-AUG-23 1K3X 1 REMARK LINK REVDAT 3 13-JUL-11 1K3X 1 VERSN REVDAT 2 24-FEB-09 1K3X 1 VERSN REVDAT 1 04-OCT-02 1K3X 0 JRNL AUTH D.O.ZHARKOV,G.GOLAN,R.GILBOA,A.S.FERNANDES,S.E.GERCHMAN, JRNL AUTH 2 J.H.KYCIA,R.A.RIEGER,A.P.GROLLMAN,G.SHOHAM JRNL TITL STRUCTURAL ANALYSIS OF AN ESCHERICHIA COLI ENDONUCLEASE VIII JRNL TITL 2 COVALENT REACTION INTERMEDIATE. JRNL REF EMBO J. V. 21 789 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 11847126 JRNL DOI 10.1093/EMBOJ/21.4.789 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.149 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 6452 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 120771 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.145 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 5614 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 105531 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2023 REMARK 3 NUCLEIC ACID ATOMS : 401 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 488 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2941.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 8 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 26922 REMARK 3 NUMBER OF RESTRAINTS : 32739 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.040 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.100 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.097 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.027 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.059 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.104 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1K3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 131559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34000 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: PDB ENTRY 1K3W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM-SULFATE, 0.1M SODIUM REMARK 280 -CITRATE PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 82.15500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 123.23250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.07750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 82.15500 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 41.07750 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 123.23250 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: B, C, 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 A 960 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1067 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1085 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 DG B 401 REMARK 465 DG B 402 REMARK 465 DG B 413 REMARK 465 DC C 421 REMARK 465 DC C 432 REMARK 465 DC C 433 REMARK 465 GLN A 214 REMARK 465 VAL A 215 REMARK 465 ASP A 216 REMARK 465 GLU A 217 REMARK 465 ASN A 218 REMARK 465 LYS A 219 REMARK 465 HIS A 220 REMARK 465 HIS A 221 REMARK 465 GLY A 222 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 GLU A 82 CG CD OE1 OE2 REMARK 470 GLN A 84 CG CD OE1 NE2 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 B 412 C4 DG B 412 C5 0.047 REMARK 500 DG C 431 C4 DG C 431 C5 0.044 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 DC B 403 OP1 - P - OP2 ANGL. DEV. = -9.9 DEGREES REMARK 500 DC B 403 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 DC B 403 C6 - N1 - C2 ANGL. DEV. = -3.0 DEGREES REMARK 500 DC B 403 C2 - N3 - C4 ANGL. DEV. = 9.9 DEGREES REMARK 500 DC B 403 N3 - C4 - C5 ANGL. DEV. = -7.5 DEGREES REMARK 500 DC B 403 C5 - C6 - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC B 403 N3 - C2 - O2 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC B 403 N3 - C4 - N4 ANGL. DEV. = 6.4 DEGREES REMARK 500 BRU B 404 C3' - O3' - P ANGL. DEV. = -8.8 DEGREES REMARK 500 DC B 406 O3' - P - OP1 ANGL. DEV. = 7.2 DEGREES REMARK 500 DC B 406 C2 - N3 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 406 N3 - C4 - C5 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA B 407 O3' - P - OP1 ANGL. DEV. = 7.5 DEGREES REMARK 500 DA B 407 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA B 407 N3 - C4 - C5 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA B 407 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 407 N1 - C6 - N6 ANGL. DEV. = -8.6 DEGREES REMARK 500 DA B 407 C5 - C6 - N6 ANGL. DEV. = 8.5 DEGREES REMARK 500 DC B 409 O4' - C1' - N1 ANGL. DEV. = -7.7 DEGREES REMARK 500 DC B 409 C2 - N3 - C4 ANGL. DEV. = 7.6 DEGREES REMARK 500 DC B 409 N3 - C4 - C5 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC B 409 N1 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC B 409 N3 - C2 - O2 ANGL. DEV. = 7.9 DEGREES REMARK 500 DC B 410 O3' - P - OP2 ANGL. DEV. = 8.2 DEGREES REMARK 500 DC B 410 C2 - N3 - C4 ANGL. DEV. = 6.2 DEGREES REMARK 500 DC B 410 N3 - C4 - C5 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC B 410 N3 - C4 - N4 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 412 C6 - N1 - C2 ANGL. DEV. = -9.1 DEGREES REMARK 500 DG B 412 N1 - C2 - N3 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG B 412 C2 - N3 - C4 ANGL. DEV. = 8.7 DEGREES REMARK 500 DG B 412 N3 - C4 - C5 ANGL. DEV. = -11.3 DEGREES REMARK 500 DG B 412 C5 - C6 - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 DG B 412 C5 - N7 - C8 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG B 412 N7 - C8 - N9 ANGL. DEV. = 10.1 DEGREES REMARK 500 DG B 412 C8 - N9 - C4 ANGL. DEV. = -7.7 DEGREES REMARK 500 DG B 412 N9 - C4 - C5 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 412 N3 - C4 - N9 ANGL. DEV. = 8.1 DEGREES REMARK 500 DG B 412 C5 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 DC C 422 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 DC C 422 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC C 422 C6 - N1 - C2 ANGL. DEV. = -3.0 DEGREES REMARK 500 DC C 422 C2 - N3 - C4 ANGL. DEV. = 9.5 DEGREES REMARK 500 DC C 422 N3 - C4 - C5 ANGL. DEV. = -7.4 DEGREES REMARK 500 DC C 422 C5 - C6 - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC C 422 N1 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC C 422 N3 - C2 - O2 ANGL. DEV. = 7.5 DEGREES REMARK 500 DC C 422 C5 - C4 - N4 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC C 422 C6 - N1 - C1' ANGL. DEV. = 9.4 DEGREES REMARK 500 DA C 423 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DG C 424 C6 - N1 - C2 ANGL. DEV. = -5.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 128 ANGLE DEVIATIONS. 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 GLN A 69 -132.26 52.39 REMARK 500 GLU A 82 92.73 -161.50 REMARK 500 SER A 104 -30.99 77.67 REMARK 500 PHE A 162 -76.28 -80.73 REMARK 500 ASN A 183 54.31 -98.64 REMARK 500 ASN A 183 58.80 -99.75 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 CYS A 237 SG REMARK 620 2 CYS A 240 SG 116.3 REMARK 620 3 CYS A 257 SG 106.4 96.4 REMARK 620 4 CYS A 260 SG 104.8 120.5 111.7 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 551 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 552 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 553 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 554 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 555 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 514 DBREF 1K3X A 1 262 UNP P50465 END8_ECOLI 1 262 DBREF 1K3X B 401 413 PDB 1K3X 1K3X 401 413 DBREF 1K3X C 421 433 PDB 1K3X 1K3X 421 433 SEQADV 1K3X THR A 34 UNP P50465 PRO 34 SEE REMARK 999 SEQADV 1K3X ARG A 112 UNP P50465 THR 112 SEE REMARK 999 SEQRES 1 B 13 DG DG DC BRU BRU DC DA BRU DC DC BRU DG DG SEQRES 1 C 13 DC DC DA DG DG DA PED DG DA DA DG DC DC SEQRES 1 A 262 PRO GLU GLY PRO GLU ILE ARG ARG ALA ALA ASP ASN LEU SEQRES 2 A 262 GLU ALA ALA ILE LYS GLY LYS PRO LEU THR ASP VAL TRP SEQRES 3 A 262 PHE ALA PHE PRO GLN LEU LYS THR TYR GLN SER GLN LEU SEQRES 4 A 262 ILE GLY GLN HIS VAL THR HIS VAL GLU THR ARG GLY LYS SEQRES 5 A 262 ALA LEU LEU THR HIS PHE SER ASN ASP LEU THR LEU TYR SEQRES 6 A 262 SER HIS ASN GLN LEU TYR GLY VAL TRP ARG VAL VAL ASP SEQRES 7 A 262 THR GLY GLU GLU PRO GLN THR THR ARG VAL LEU ARG VAL SEQRES 8 A 262 LYS LEU GLN THR ALA ASP LYS THR ILE LEU LEU TYR SER SEQRES 9 A 262 ALA SER ASP ILE GLU MET LEU ARG PRO GLU GLN LEU THR SEQRES 10 A 262 THR HIS PRO PHE LEU GLN ARG VAL GLY PRO ASP VAL LEU SEQRES 11 A 262 ASP PRO ASN LEU THR PRO GLU VAL VAL LYS GLU ARG LEU SEQRES 12 A 262 LEU SER PRO ARG PHE ARG ASN ARG GLN PHE ALA GLY LEU SEQRES 13 A 262 LEU LEU ASP GLN ALA PHE LEU ALA GLY LEU GLY ASN TYR SEQRES 14 A 262 LEU ARG VAL GLU ILE LEU TRP GLN VAL GLY LEU THR GLY SEQRES 15 A 262 ASN HIS LYS ALA LYS ASP LEU ASN ALA ALA GLN LEU ASP SEQRES 16 A 262 ALA LEU ALA HIS ALA LEU LEU GLU ILE PRO ARG PHE SER SEQRES 17 A 262 TYR ALA THR ARG GLY GLN VAL ASP GLU ASN LYS HIS HIS SEQRES 18 A 262 GLY ALA LEU PHE ARG PHE LYS VAL PHE HIS ARG ASP GLY SEQRES 19 A 262 GLU PRO CYS GLU ARG CYS GLY SER ILE ILE GLU LYS THR SEQRES 20 A 262 THR LEU SER SER ARG PRO PHE TYR TRP CYS PRO GLY CYS SEQRES 21 A 262 GLN HIS MODRES 1K3X BRU B 404 DU MODRES 1K3X BRU B 405 DU MODRES 1K3X BRU B 408 DU MODRES 1K3X BRU B 411 DU HET BRU B 404 20 HET BRU B 405 20 HET BRU B 408 20 HET BRU B 411 20 HET PED C 427 11 HET ZN A 501 1 HET SO4 A 551 5 HET SO4 A 552 5 HET SO4 A 553 5 HET SO4 A 554 5 HET SO4 A 555 5 HET GOL A 511 6 HET GOL A 512 6 HET GOL A 513 6 HET GOL A 514 6 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM PED PENTANE-3,4-DIOL-5-PHOSPHATE HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN PED OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 BRU 4(C9 H12 BR N2 O8 P) FORMUL 2 PED C5 H13 O6 P FORMUL 4 ZN ZN 2+ FORMUL 5 SO4 5(O4 S 2-) FORMUL 10 GOL 4(C3 H8 O3) FORMUL 14 HOH *488(H2 O) HELIX 1 1 GLU A 2 LYS A 18 1 17 HELIX 2 2 PHE A 29 LYS A 33 5 5 HELIX 3 3 THR A 34 ILE A 40 1 7 HELIX 4 4 GLU A 114 HIS A 119 1 6 HELIX 5 5 HIS A 119 VAL A 125 1 7 HELIX 6 6 THR A 135 SER A 145 1 11 HELIX 7 7 GLN A 152 LEU A 157 1 6 HELIX 8 8 GLY A 167 GLY A 179 1 13 HELIX 9 9 LYS A 185 LEU A 189 5 5 HELIX 10 10 ASN A 190 ARG A 212 1 23 SHEET 1 A 4 ASP A 24 PHE A 27 0 SHEET 2 A 4 LEU A 89 GLN A 94 -1 O GLN A 94 N ASP A 24 SHEET 3 A 4 LYS A 98 TYR A 103 -1 O ILE A 100 N LEU A 93 SHEET 4 A 4 VAL A 73 ASP A 78 -1 N VAL A 73 O TYR A 103 SHEET 1 B 4 VAL A 44 ARG A 50 0 SHEET 2 B 4 ALA A 53 PHE A 58 -1 O LEU A 55 N GLU A 48 SHEET 3 B 4 THR A 63 HIS A 67 -1 O SER A 66 N LEU A 54 SHEET 4 B 4 ASP A 107 LEU A 111 -1 O LEU A 111 N THR A 63 SHEET 1 C 2 GLU A 245 LEU A 249 0 SHEET 2 C 2 ARG A 252 TRP A 256 -1 O TRP A 256 N GLU A 245 LINK O3' DC B 403 P BRU B 404 1555 1555 1.63 LINK O3' BRU B 404 P BRU B 405 1555 1555 1.64 LINK O3' BRU B 405 P DC B 406 1555 1555 1.59 LINK O3' DA B 407 P BRU B 408 1555 1555 1.62 LINK O3' BRU B 408 P DC B 409 1555 1555 1.62 LINK O3' DC B 410 P BRU B 411 1555 1555 1.63 LINK O3' BRU B 411 P DG B 412 1555 1555 1.64 LINK O3' DA C 426 P PED C 427 1555 1555 1.61 LINK O3' PED C 427 P DG C 428 1555 1555 1.60 LINK C1' PED C 427 N PRO A 1 1555 1555 1.40 LINK SG CYS A 237 ZN ZN A 501 1555 1555 2.36 LINK SG CYS A 240 ZN ZN A 501 1555 1555 2.31 LINK SG CYS A 257 ZN ZN A 501 1555 1555 2.33 LINK SG CYS A 260 ZN ZN A 501 1555 1555 2.31 SITE 1 AC1 4 CYS A 237 CYS A 240 CYS A 257 CYS A 260 SITE 1 AC2 5 ARG A 8 ASN A 12 HOH A 657 HOH A1022 SITE 2 AC2 5 HOH A1025 SITE 1 AC3 8 ARG A 112 LYS A 140 ALA A 191 ASP A 195 SITE 2 AC3 8 HOH A 665 HOH A 757 HOH A 856 HOH A 957 SITE 1 AC4 6 ASN A 190 ALA A 191 HOH A 630 HOH A 828 SITE 2 AC4 6 HOH A 884 HOH A 941 SITE 1 AC5 3 PRO A 1 HOH A 681 HOH A 961 SITE 1 AC6 5 HOH A 648 HOH A 652 HOH A 734 HOH A 994 SITE 2 AC6 5 HOH A1071 SITE 1 AC7 4 ARG A 147 ARG A 151 HOH A 685 HOH A 773 SITE 1 AC8 7 ASP A 195 HIS A 199 HOH A 684 HOH A 691 SITE 2 AC8 7 HOH A 722 HOH A 752 HOH A 932 SITE 1 AC9 10 SER A 37 GLN A 38 GLY A 179 LEU A 180 SITE 2 AC9 10 HIS A 184 GLN A 193 HIS A 262 HOH A 671 SITE 3 AC9 10 HOH A 689 HOH A 737 SITE 1 BC1 6 THR A 117 ARG A 142 HOH A 655 HOH A 711 SITE 2 BC1 6 HOH A 998 HOH A1054 CRYST1 76.495 76.495 164.310 90.00 90.00 90.00 P 43 2 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 0.013073 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013073 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006086 0.00000