HEADER TRANSFERASE/TRANSFERASE INHIBITOR 23-DEC-10 3Q4L TITLE STRUCTURE OF A SMALL PEPTIDE LIGAND BOUND TO E.COLI DNA SLIDING CLAMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE III SUBUNIT BETA; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PEPTIDE LIGAND; COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: DNAN, B3701, JW3678; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS DNA POLYMERASE, SLIDING CLAMP, PROCESSIVITY FACTORS, LIGAND BINDING, KEYWDS 2 DNA REPLICATION, DNA-DIRECTED DNA POLYMERASE, KEYWDS 3 NUCLEOTIDYLTRANSFERASE, TRANSFERASE, TRANSFERASE-PEPTIDE COMPLEX, KEYWDS 4 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.WOLFF,V.OLIERIC,J.P.BRIAND,O.CHALOIN,A.DEJAEGERE,P.DUMAS,E.ENNIFAR, AUTHOR 2 G.GUICHARD,J.WAGNER,D.BURNOUF REVDAT 2 20-MAR-13 3Q4L 1 JRNL REVDAT 1 28-DEC-11 3Q4L 0 JRNL AUTH P.WOLFF,V.OLIERIC,J.P.BRIAND,O.CHALOIN,A.DEJAEGERE,P.DUMAS, JRNL AUTH 2 E.ENNIFAR,G.GUICHARD,J.WAGNER,D.Y.BURNOUF JRNL TITL STRUCTURE-BASED DESIGN OF SHORT PEPTIDE LIGANDS BINDING ONTO JRNL TITL 2 THE E. COLI PROCESSIVITY RING. JRNL REF J.MED.CHEM. V. 54 4627 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21619076 JRNL DOI 10.1021/JM200311M REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.8.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 54134 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2706 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.00 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3864 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2379 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3671 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2545 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.99 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 193 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5590 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 296 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.91330 REMARK 3 B22 (A**2) : 1.35230 REMARK 3 B33 (A**2) : 8.56100 REMARK 3 B12 (A**2) : 2.46590 REMARK 3 B13 (A**2) : 2.97530 REMARK 3 B23 (A**2) : 4.79850 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5722 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 7764 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1940 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 151 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 853 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5722 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 2 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 759 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 6666 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.13 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.14 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.95 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3Q4L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-10. REMARK 100 THE RCSB ID CODE IS RCSB063186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.72400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.0, 0.1M CACL2, 30% PEG REMARK 280 400, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, C 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 400 REMARK 400 COMPOUND REMARK 400 THE SHORT PEPTIDE BINDS ONTO PROCESSIVITY FACTOR BETA CLAMP, REMARK 400 INHIBITING BETA-DEPENDENT ELONGATION ACTIVITY REMARK 400 REMARK 400 THE PEPTIDE LIGAND IS OLIGOPEPTIDE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: PEPTIDE LIGAND REMARK 400 CHAIN: C, D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 LEU A 21 REMARK 465 GLY A 22 REMARK 465 GLY A 23 REMARK 465 ARG A 24 REMARK 465 ALA B -1 REMARK 465 GLY B 22 REMARK 465 GLY B 23 REMARK 465 ARG B 24 REMARK 465 LEU B 366 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 LYS A 12 CG CD CE NZ REMARK 470 GLN A 15 CG CD OE1 NE2 REMARK 470 THR A 26 OG1 CG2 REMARK 470 ASP A 39 CG OD1 OD2 REMARK 470 ARG A 105 NE CZ NH1 NH2 REMARK 470 ASN A 118 CG OD1 ND2 REMARK 470 LEU A 119 CG CD1 CD2 REMARK 470 ASP A 120 CG OD1 OD2 REMARK 470 ARG A 137 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 PRO A 183 CG CD REMARK 470 GLU A 202 CG CD OE1 OE2 REMARK 470 ASP A 211 CG OD1 OD2 REMARK 470 ASN A 212 CG OD1 ND2 REMARK 470 VAL A 227 CG1 CG2 REMARK 470 ARG A 240 NE CZ NH1 NH2 REMARK 470 LYS A 250 CG CD CE NZ REMARK 470 ASP A 261 CG OD1 OD2 REMARK 470 GLN A 299 CD OE1 NE2 REMARK 470 GLU A 316 CG CD OE1 OE2 REMARK 470 GLN A 355 CG CD OE1 NE2 REMARK 470 LEU A 366 CG CD1 CD2 REMARK 470 THR B 26 OG1 CG2 REMARK 470 LEU B 27 CG CD1 CD2 REMARK 470 ASP B 39 CG OD1 OD2 REMARK 470 GLU B 50 CG CD OE1 OE2 REMARK 470 GLU B 93 CG CD OE1 OE2 REMARK 470 GLU B 95 CG CD OE1 OE2 REMARK 470 ASN B 118 CG OD1 ND2 REMARK 470 LEU B 119 CG CD1 CD2 REMARK 470 ASP B 120 CG OD1 OD2 REMARK 470 ASP B 121 CG OD1 OD2 REMARK 470 ARG B 137 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 165 CG CD OE1 OE2 REMARK 470 ILE B 184 CG1 CG2 CD1 REMARK 470 ARG B 205 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 208 CG OD1 OD2 REMARK 470 ASP B 211 CG OD1 OD2 REMARK 470 VAL B 227 CG1 CG2 REMARK 470 ASP B 238 CG OD1 OD2 REMARK 470 ARG B 240 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 250 CG CD CE NZ REMARK 470 GLU B 257 CG CD OE1 OE2 REMARK 470 GLN B 299 CG CD OE1 NE2 REMARK 470 GLU B 301 CG CD OE1 OE2 REMARK 470 GLN B 355 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 LEU C 371 N LEU C 371 CA 0.150 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 ASP C 370 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 LEU D 371 CB - CG - CD2 ANGL. DEV. = 12.2 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 THR A 26 -34.59 -149.71 REMARK 500 ASP A 39 70.82 31.82 REMARK 500 LEU A 49 -28.16 80.21 REMARK 500 ARG A 279 18.45 58.34 REMARK 500 THR A 341 -73.45 -120.58 REMARK 500 ASP B 39 69.86 33.54 REMARK 500 LEU B 49 -28.72 81.31 REMARK 500 THR B 341 -72.87 -119.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ILE A 184 24.6 L L OUTSIDE RANGE REMARK 500 VAL A 247 22.5 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH D 402 DISTANCE = 5.25 ANGSTROMS 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 NA B 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 631 O REMARK 620 2 HOH B 541 O 93.6 REMARK 620 3 HOH B 510 O 170.0 88.7 REMARK 620 4 HOH B 555 O 83.0 142.6 89.2 REMARK 620 5 SER B 345 OG 91.3 72.9 80.1 69.9 REMARK 620 6 HOH B 628 O 120.9 80.3 69.0 132.9 139.3 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 NA B 367 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF PEPTIDE LIGAND REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF PEPTIDE LIGAND REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OK7 RELATED DB: PDB REMARK 900 RELATED ID: 3Q4J RELATED DB: PDB REMARK 900 RELATED ID: 3Q4K RELATED DB: PDB REMARK 900 RELATED ID: 3D1E RELATED DB: PDB REMARK 900 RELATED ID: 3D1F RELATED DB: PDB REMARK 900 RELATED ID: 3D1G RELATED DB: PDB DBREF 3Q4L A 1 366 UNP P0A988 DPO3B_ECOLI 1 366 DBREF 3Q4L B 1 366 UNP P0A988 DPO3B_ECOLI 1 366 DBREF 3Q4L C 367 372 PDB 3Q4L 3Q4L 367 372 DBREF 3Q4L D 367 372 PDB 3Q4L 3Q4L 367 372 SEQADV 3Q4L ALA A -1 UNP P0A988 EXPRESSION TAG SEQADV 3Q4L ALA A 0 UNP P0A988 EXPRESSION TAG SEQADV 3Q4L ALA B -1 UNP P0A988 EXPRESSION TAG SEQADV 3Q4L ALA B 0 UNP P0A988 EXPRESSION TAG SEQRES 1 A 368 ALA ALA MET LYS PHE THR VAL GLU ARG GLU HIS LEU LEU SEQRES 2 A 368 LYS PRO LEU GLN GLN VAL SER GLY PRO LEU GLY GLY ARG SEQRES 3 A 368 PRO THR LEU PRO ILE LEU GLY ASN LEU LEU LEU GLN VAL SEQRES 4 A 368 ALA ASP GLY THR LEU SER LEU THR GLY THR ASP LEU GLU SEQRES 5 A 368 MET GLU MET VAL ALA ARG VAL ALA LEU VAL GLN PRO HIS SEQRES 6 A 368 GLU PRO GLY ALA THR THR VAL PRO ALA ARG LYS PHE PHE SEQRES 7 A 368 ASP ILE CYS ARG GLY LEU PRO GLU GLY ALA GLU ILE ALA SEQRES 8 A 368 VAL GLN LEU GLU GLY GLU ARG MET LEU VAL ARG SER GLY SEQRES 9 A 368 ARG SER ARG PHE SER LEU SER THR LEU PRO ALA ALA ASP SEQRES 10 A 368 PHE PRO ASN LEU ASP ASP TRP GLN SER GLU VAL GLU PHE SEQRES 11 A 368 THR LEU PRO GLN ALA THR MET LYS ARG LEU ILE GLU ALA SEQRES 12 A 368 THR GLN PHE SER MET ALA HIS GLN ASP VAL ARG TYR TYR SEQRES 13 A 368 LEU ASN GLY MET LEU PHE GLU THR GLU GLY GLU GLU LEU SEQRES 14 A 368 ARG THR VAL ALA THR ASP GLY HIS ARG LEU ALA VAL CYS SEQRES 15 A 368 SER MET PRO ILE GLY GLN SER LEU PRO SER HIS SER VAL SEQRES 16 A 368 ILE VAL PRO ARG LYS GLY VAL ILE GLU LEU MET ARG MET SEQRES 17 A 368 LEU ASP GLY GLY ASP ASN PRO LEU ARG VAL GLN ILE GLY SEQRES 18 A 368 SER ASN ASN ILE ARG ALA HIS VAL GLY ASP PHE ILE PHE SEQRES 19 A 368 THR SER LYS LEU VAL ASP GLY ARG PHE PRO ASP TYR ARG SEQRES 20 A 368 ARG VAL LEU PRO LYS ASN PRO ASP LYS HIS LEU GLU ALA SEQRES 21 A 368 GLY CYS ASP LEU LEU LYS GLN ALA PHE ALA ARG ALA ALA SEQRES 22 A 368 ILE LEU SER ASN GLU LYS PHE ARG GLY VAL ARG LEU TYR SEQRES 23 A 368 VAL SER GLU ASN GLN LEU LYS ILE THR ALA ASN ASN PRO SEQRES 24 A 368 GLU GLN GLU GLU ALA GLU GLU ILE LEU ASP VAL THR TYR SEQRES 25 A 368 SER GLY ALA GLU MET GLU ILE GLY PHE ASN VAL SER TYR SEQRES 26 A 368 VAL LEU ASP VAL LEU ASN ALA LEU LYS CYS GLU ASN VAL SEQRES 27 A 368 ARG MET MET LEU THR ASP SER VAL SER SER VAL GLN ILE SEQRES 28 A 368 GLU ASP ALA ALA SER GLN SER ALA ALA TYR VAL VAL MET SEQRES 29 A 368 PRO MET ARG LEU SEQRES 1 B 368 ALA ALA MET LYS PHE THR VAL GLU ARG GLU HIS LEU LEU SEQRES 2 B 368 LYS PRO LEU GLN GLN VAL SER GLY PRO LEU GLY GLY ARG SEQRES 3 B 368 PRO THR LEU PRO ILE LEU GLY ASN LEU LEU LEU GLN VAL SEQRES 4 B 368 ALA ASP GLY THR LEU SER LEU THR GLY THR ASP LEU GLU SEQRES 5 B 368 MET GLU MET VAL ALA ARG VAL ALA LEU VAL GLN PRO HIS SEQRES 6 B 368 GLU PRO GLY ALA THR THR VAL PRO ALA ARG LYS PHE PHE SEQRES 7 B 368 ASP ILE CYS ARG GLY LEU PRO GLU GLY ALA GLU ILE ALA SEQRES 8 B 368 VAL GLN LEU GLU GLY GLU ARG MET LEU VAL ARG SER GLY SEQRES 9 B 368 ARG SER ARG PHE SER LEU SER THR LEU PRO ALA ALA ASP SEQRES 10 B 368 PHE PRO ASN LEU ASP ASP TRP GLN SER GLU VAL GLU PHE SEQRES 11 B 368 THR LEU PRO GLN ALA THR MET LYS ARG LEU ILE GLU ALA SEQRES 12 B 368 THR GLN PHE SER MET ALA HIS GLN ASP VAL ARG TYR TYR SEQRES 13 B 368 LEU ASN GLY MET LEU PHE GLU THR GLU GLY GLU GLU LEU SEQRES 14 B 368 ARG THR VAL ALA THR ASP GLY HIS ARG LEU ALA VAL CYS SEQRES 15 B 368 SER MET PRO ILE GLY GLN SER LEU PRO SER HIS SER VAL SEQRES 16 B 368 ILE VAL PRO ARG LYS GLY VAL ILE GLU LEU MET ARG MET SEQRES 17 B 368 LEU ASP GLY GLY ASP ASN PRO LEU ARG VAL GLN ILE GLY SEQRES 18 B 368 SER ASN ASN ILE ARG ALA HIS VAL GLY ASP PHE ILE PHE SEQRES 19 B 368 THR SER LYS LEU VAL ASP GLY ARG PHE PRO ASP TYR ARG SEQRES 20 B 368 ARG VAL LEU PRO LYS ASN PRO ASP LYS HIS LEU GLU ALA SEQRES 21 B 368 GLY CYS ASP LEU LEU LYS GLN ALA PHE ALA ARG ALA ALA SEQRES 22 B 368 ILE LEU SER ASN GLU LYS PHE ARG GLY VAL ARG LEU TYR SEQRES 23 B 368 VAL SER GLU ASN GLN LEU LYS ILE THR ALA ASN ASN PRO SEQRES 24 B 368 GLU GLN GLU GLU ALA GLU GLU ILE LEU ASP VAL THR TYR SEQRES 25 B 368 SER GLY ALA GLU MET GLU ILE GLY PHE ASN VAL SER TYR SEQRES 26 B 368 VAL LEU ASP VAL LEU ASN ALA LEU LYS CYS GLU ASN VAL SEQRES 27 B 368 ARG MET MET LEU THR ASP SER VAL SER SER VAL GLN ILE SEQRES 28 B 368 GLU ASP ALA ALA SER GLN SER ALA ALA TYR VAL VAL MET SEQRES 29 B 368 PRO MET ARG LEU SEQRES 1 C 6 ACE GLN ALC ASP LEU ZCL SEQRES 1 D 6 ACE GLN ALC ASP LEU ZCL MODRES 3Q4L ALC C 369 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID MODRES 3Q4L ZCL C 372 PHE 3,4-DICHLORO-L-PHENYLALANINE MODRES 3Q4L ALC D 369 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID MODRES 3Q4L ZCL D 372 PHE 3,4-DICHLORO-L-PHENYLALANINE HET ACE C 367 3 HET ALC C 369 11 HET ZCL C 372 14 HET ACE D 367 3 HET ALC D 369 11 HET ZCL D 372 14 HET NA B 401 1 HETNAM ACE ACETYL GROUP HETNAM ALC 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID HETNAM ZCL 3,4-DICHLORO-L-PHENYLALANINE HETNAM NA SODIUM ION FORMUL 3 ACE 2(C2 H4 O) FORMUL 3 ALC 2(C9 H17 N O2) FORMUL 3 ZCL 2(C9 H9 CL2 N O2) FORMUL 5 NA NA 1+ FORMUL 6 HOH *296(H2 O) HELIX 1 1 ARG A 7 SER A 18 1 12 HELIX 2 2 LEU A 27 LEU A 30 5 4 HELIX 3 3 ALA A 72 LEU A 82 1 11 HELIX 4 4 PRO A 112 PHE A 116 5 5 HELIX 5 5 PRO A 131 GLN A 143 1 13 HELIX 6 6 PHE A 144 MET A 146 5 3 HELIX 7 7 ARG A 152 GLY A 157 5 6 HELIX 8 8 PRO A 196 MET A 206 1 11 HELIX 9 9 ASP A 243 LEU A 248 5 6 HELIX 10 10 CYS A 260 ILE A 272 1 13 HELIX 11 11 VAL A 321 LEU A 331 1 11 HELIX 12 12 ARG B 7 SER B 18 1 12 HELIX 13 13 LEU B 27 LEU B 30 5 4 HELIX 14 14 ALA B 72 LEU B 82 1 11 HELIX 15 15 PRO B 112 PHE B 116 5 5 HELIX 16 16 PRO B 131 GLN B 143 1 13 HELIX 17 17 PHE B 144 MET B 146 5 3 HELIX 18 18 ARG B 152 GLY B 157 5 6 HELIX 19 19 PRO B 196 MET B 206 1 11 HELIX 20 20 ASP B 243 LEU B 248 1 6 HELIX 21 21 CYS B 260 ILE B 272 1 13 HELIX 22 22 VAL B 321 LEU B 331 1 11 SHEET 1 A 8 LYS A 2 GLU A 6 0 SHEET 2 A 8 GLU A 87 GLU A 93 -1 O VAL A 90 N PHE A 3 SHEET 3 A 8 ARG A 96 SER A 101 -1 O LEU A 98 N GLN A 91 SHEET 4 A 8 SER A 104 SER A 109 -1 O LEU A 108 N MET A 97 SHEET 5 A 8 GLU B 301 ASP B 307 -1 O GLU B 303 N ARG A 105 SHEET 6 A 8 GLN B 289 ASN B 295 -1 N ILE B 292 O GLU B 304 SHEET 7 A 8 GLY B 280 SER B 286 -1 N ARG B 282 O THR B 293 SHEET 8 A 8 MET B 315 ASN B 320 -1 O MET B 315 N VAL B 285 SHEET 1 B 8 GLY A 66 PRO A 71 0 SHEET 2 B 8 ASN A 32 ALA A 38 -1 N LEU A 35 O THR A 68 SHEET 3 B 8 THR A 41 THR A 47 -1 O SER A 43 N GLN A 36 SHEET 4 B 8 MET A 51 ALA A 58 -1 O VAL A 57 N LEU A 42 SHEET 5 B 8 PHE A 230 LYS A 235 -1 O THR A 233 N GLU A 52 SHEET 6 B 8 ASN A 222 VAL A 227 -1 N ALA A 225 O PHE A 232 SHEET 7 B 8 LEU A 214 ILE A 218 -1 N ARG A 215 O HIS A 226 SHEET 8 B 8 VAL A 126 LEU A 130 -1 N PHE A 128 O VAL A 216 SHEET 1 C 6 LYS A 254 GLY A 259 0 SHEET 2 C 6 ASN A 335 LEU A 340 -1 O MET A 338 N LEU A 256 SHEET 3 C 6 VAL A 347 ASP A 351 -1 O GLN A 348 N MET A 339 SHEET 4 C 6 SER A 354 VAL A 361 -1 O TYR A 359 N ILE A 349 SHEET 5 C 6 ARG A 176 VAL A 195 -1 N LEU A 177 O VAL A 360 SHEET 6 C 6 MET A 158 THR A 172 -1 O GLU A 165 N ILE A 184 SHEET 1 D 8 MET A 315 ASN A 320 0 SHEET 2 D 8 GLY A 280 SER A 286 -1 N VAL A 285 O MET A 315 SHEET 3 D 8 GLN A 289 ASN A 295 -1 O THR A 293 N ARG A 282 SHEET 4 D 8 GLU A 301 ASP A 307 -1 O GLU A 304 N ILE A 292 SHEET 5 D 8 SER B 104 SER B 109 -1 O SER B 107 N GLU A 301 SHEET 6 D 8 ARG B 96 SER B 101 -1 N MET B 97 O LEU B 108 SHEET 7 D 8 GLU B 87 GLU B 93 -1 N GLN B 91 O LEU B 98 SHEET 8 D 8 LYS B 2 GLU B 6 -1 N PHE B 3 O VAL B 90 SHEET 1 E 8 GLY B 66 PRO B 71 0 SHEET 2 E 8 ASN B 32 ALA B 38 -1 N LEU B 35 O THR B 68 SHEET 3 E 8 THR B 41 THR B 47 -1 O SER B 43 N GLN B 36 SHEET 4 E 8 MET B 51 ALA B 58 -1 O VAL B 57 N LEU B 42 SHEET 5 E 8 PHE B 230 LYS B 235 -1 O THR B 233 N GLU B 52 SHEET 6 E 8 ASN B 222 VAL B 227 -1 N ALA B 225 O PHE B 232 SHEET 7 E 8 LEU B 214 ILE B 218 -1 N ARG B 215 O HIS B 226 SHEET 8 E 8 VAL B 126 LEU B 130 -1 N PHE B 128 O VAL B 216 SHEET 1 F 7 THR B 309 TYR B 310 0 SHEET 2 F 7 LYS B 254 GLY B 259 -1 N GLU B 257 O THR B 309 SHEET 3 F 7 ASN B 335 LEU B 340 -1 O MET B 338 N LEU B 256 SHEET 4 F 7 VAL B 347 ASP B 351 -1 O GLN B 348 N MET B 339 SHEET 5 F 7 SER B 354 VAL B 361 -1 O TYR B 359 N ILE B 349 SHEET 6 F 7 ARG B 176 VAL B 195 -1 N LEU B 177 O VAL B 360 SHEET 7 F 7 MET B 158 THR B 172 -1 O GLU B 165 N ILE B 184 LINK C GLN C 368 N ALC C 369 1555 1555 1.34 LINK C ALC C 369 N ASP C 370 1555 1555 1.32 LINK C LEU C 371 N ZCL C 372 1555 1555 1.32 LINK C GLN D 368 N ALC D 369 1555 1555 1.35 LINK C ALC D 369 N ASP D 370 1555 1555 1.31 LINK C LEU D 371 N ZCL D 372 1555 1555 1.29 LINK C ACE C 367 N GLN C 368 1555 1555 1.30 LINK C ACE D 367 N GLN D 368 1555 1555 1.30 LINK NA NA B 401 O HOH B 631 1555 1555 2.23 LINK NA NA B 401 O HOH B 541 1555 1555 2.24 LINK NA NA B 401 O HOH B 510 1555 1555 2.28 LINK NA NA B 401 O HOH B 555 1555 1555 2.35 LINK OG SER B 345 NA NA B 401 1555 1555 2.38 LINK NA NA B 401 O HOH B 628 1555 1555 2.51 SITE 1 AC1 2 GLU A 166 SER B 345 SITE 1 AC2 18 THR A 172 GLY A 174 HIS A 175 LEU A 177 SITE 2 AC2 18 PRO A 242 ASP A 243 TYR A 244 VAL A 247 SITE 3 AC2 18 TYR A 323 GLU A 334 ASN A 335 ALA A 353 SITE 4 AC2 18 MET A 362 PRO A 363 MET A 364 ARG A 365 SITE 5 AC2 18 HOH A 420 HOH A 453 SITE 1 AC3 16 THR B 172 GLY B 174 HIS B 175 ARG B 176 SITE 2 AC3 16 LEU B 177 PRO B 242 ASP B 243 VAL B 247 SITE 3 AC3 16 TYR B 323 GLU B 334 ASN B 335 VAL B 360 SITE 4 AC3 16 MET B 362 PRO B 363 MET B 364 ARG B 365 CRYST1 34.840 79.570 81.640 65.28 75.26 82.22 P 1 2 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 0.028703 -0.003922 -0.006527 0.00000 SCALE2 0.000000 0.012684 -0.005544 0.00000 SCALE3 0.000000 0.000000 0.013823 0.00000