HEADER CHAPERONE, PEPTIDE BINDING PROTEIN 09-JUL-08 3DPP TITLE CRYSTAL STRUCTURE OF THE SUBSTRATE BINDING DOMAIN OF E. COLI DNAK IN TITLE 2 COMPLEX WITH A LONG PYRRHOCORICIN-DERIVED INHIBITOR PEPTIDE (FORM A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAPERONE PROTEIN DNAK; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SUBSTRATE BINDING DOMAIN (UNP RESIDUES 389 TO 607); COMPND 5 SYNONYM: HEAT SHOCK PROTEIN 70, HEAT SHOCK 70 KDA PROTEIN, HSP70; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: INHIBITOR PEPTIDE; COMPND 9 CHAIN: C, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: DNAK, GROP, GRPF, SEG, B0014, JW0013; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: THE PEPTIDE WAS PYRRHOCORICIN-DERIVED. KEYWDS MOLECULAR CHAPERONE, DNAK, HSP70, SUBSTRATE-BINDING DOMAIN, KEYWDS 2 PYRRHOCORICIN INHIBITOR, ATP-BINDING, CHAPERONE, CYTOPLASM, DNA KEYWDS 3 REPLICATION, MEMBRANE, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, STRESS KEYWDS 4 RESPONSE, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.ROUJEINIKOVA REVDAT 3 30-AUG-23 3DPP 1 REMARK LINK REVDAT 2 25-OCT-17 3DPP 1 REMARK REVDAT 1 10-MAR-09 3DPP 0 JRNL AUTH M.LIEBSCHER,A.ROUJEINIKOVA JRNL TITL ALLOSTERIC COUPLING BETWEEN THE LID AND INTERDOMAIN LINKER JRNL TITL 2 IN DNAK REVEALED BY INHIBITOR BINDING STUDIES. JRNL REF J.BACTERIOL. V. 191 1456 2009 JRNL REFN ISSN 0021-9193 JRNL PMID 19103929 JRNL DOI 10.1128/JB.01131-08 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 17451 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) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.316 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 892 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1194 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3363 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 309 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.40000 REMARK 3 B22 (A**2) : 1.26000 REMARK 3 B33 (A**2) : 1.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.975 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.400 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.234 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.878 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.871 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3481 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2300 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4713 ; 2.041 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5699 ; 2.049 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 7.854 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;38.713 ;25.946 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 628 ;18.152 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.204 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 557 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3873 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 582 ; 0.003 ; 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): 2273 ; 1.856 ; 4.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 908 ; 0.505 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3650 ; 2.841 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1208 ; 2.342 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1063 ; 3.565 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3DPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, D*TREK REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17463 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.21700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3DPO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M AMMONIUM SULFATE, 100 MM CITRIC REMARK 280 ACID , PH 5.0, VAPOR DIFFUSION, SITTING 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 38.93500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 79.56000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.93500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 79.56000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 ILE A 601 REMARK 465 ALA A 602 REMARK 465 GLN A 603 REMARK 465 GLN A 604 REMARK 465 GLN A 605 REMARK 465 HIS A 606 REMARK 465 ALA A 607 REMARK 465 GLN B 603 REMARK 465 GLN B 604 REMARK 465 GLN B 605 REMARK 465 HIS B 606 REMARK 465 ALA B 607 REMARK 465 VAL C -2 REMARK 465 ASP C -1 REMARK 465 ILE C 13 REMARK 465 TYR C 14 REMARK 465 ASN C 15 REMARK 465 ARG C 16 REMARK 465 ASN C 17 REMARK 465 VAL D -2 REMARK 465 ASP D -1 REMARK 465 PRO D 9 REMARK 465 PRO D 10 REMARK 465 ARG D 11 REMARK 465 PRO D 12 REMARK 465 ILE D 13 REMARK 465 TYR D 14 REMARK 465 ASN D 15 REMARK 465 ARG D 16 REMARK 465 ASN D 17 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 GLN A 513 CG CD OE1 NE2 REMARK 470 GLU A 524 CG CD OE1 OE2 REMARK 470 LYS A 548 CG CD CE NZ REMARK 470 GLU A 551 CG CD OE1 OE2 REMARK 470 GLU A 552 CG CD OE1 OE2 REMARK 470 LEU A 557 CG CD1 CD2 REMARK 470 LYS A 562 CG CD CE NZ REMARK 470 GLN A 596 CG CD OE1 NE2 REMARK 470 LYS A 597 CG CD CE NZ REMARK 470 MET A 599 CG SD CE REMARK 470 GLU A 600 CG CD OE1 OE2 REMARK 470 GLU B 520 CG CD OE1 OE2 REMARK 470 LYS B 548 CG CD CE NZ REMARK 470 GLU B 552 CG CD OE1 OE2 REMARK 470 LYS C 0 CG CD CE NZ REMARK 470 LYS D 0 CG CD CE NZ 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 C ARG C 11 CD PRO C 12 1.49 REMARK 500 O ARG C 11 CD PRO C 12 1.69 REMARK 500 O HOH A 54 O HOH A 348 1.85 REMARK 500 O HOH B 652 O HOH B 726 1.91 REMARK 500 O ASP A 555 N LEU A 557 1.95 REMARK 500 OE2 GLU B 579 O HOH B 764 2.01 REMARK 500 O PRO A 558 N ASP A 560 2.02 REMARK 500 O HOH A 19 O HOH A 379 2.02 REMARK 500 O HOH B 763 O HOH B 765 2.03 REMARK 500 O HOH B 675 O HOH B 716 2.05 REMARK 500 O HOH B 715 O HOH B 734 2.07 REMARK 500 O LEU A 557 N ALA A 559 2.10 REMARK 500 O HOH B 768 O HOH B 772 2.11 REMARK 500 O HOH A 151 O HOH A 289 2.12 REMARK 500 O HOH B 679 O HOH C 20 2.12 REMARK 500 O HOH A 158 O HOH A 204 2.13 REMARK 500 O HOH A 274 O HOH A 388 2.13 REMARK 500 O HOH A 174 O HOH B 706 2.16 REMARK 500 O HOH A 195 O HOH A 279 2.18 REMARK 500 O HOH A 74 O HOH A 381 2.19 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 C 2 C ALC C 3 N -0.157 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 B 445 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ALC C 3 C - N - CA ANGL. DEV. = 19.6 DEGREES REMARK 500 PRO C 12 C - N - CA ANGL. DEV. = 38.0 DEGREES REMARK 500 PRO C 12 C - N - CD ANGL. DEV. = -64.5 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 LEU A 411 -32.13 -150.75 REMARK 500 THR A 420 143.13 -171.40 REMARK 500 SER A 427 -160.98 -124.95 REMARK 500 PRO A 464 107.25 -54.46 REMARK 500 ASP A 479 -168.85 -78.38 REMARK 500 ASN A 492 -73.30 -64.74 REMARK 500 GLU A 551 20.36 -69.12 REMARK 500 ASP A 555 37.41 -75.79 REMARK 500 LYS A 556 28.50 -38.97 REMARK 500 LEU A 557 -178.94 55.02 REMARK 500 PRO A 558 19.71 -45.96 REMARK 500 ALA A 559 -10.81 51.16 REMARK 500 GLN A 593 -72.88 -71.90 REMARK 500 VAL A 594 42.52 -68.11 REMARK 500 SER A 595 13.31 -141.04 REMARK 500 SER B 427 -158.65 -143.37 REMARK 500 ASP B 431 131.43 -27.08 REMARK 500 LYS B 502 152.64 -49.06 REMARK 500 GLU B 530 -78.46 160.95 REMARK 500 ILE B 584 -73.35 -68.57 REMARK 500 GLU B 585 -28.55 -33.66 REMARK 500 GLU B 600 -77.36 -83.58 REMARK 500 ILE B 601 -68.10 -16.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE B 529 GLU B 530 -70.01 REMARK 500 PRO C 10 ARG C 11 -140.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TYR D 2 -13.00 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 SO4 A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DPO RELATED DB: PDB REMARK 900 RELATED ID: 3DPQ RELATED DB: PDB DBREF 3DPP A 389 607 UNP P0A6Y8 DNAK_ECOLI 389 607 DBREF 3DPP B 389 607 UNP P0A6Y8 DNAK_ECOLI 389 607 DBREF 3DPP C -2 17 PDB 3DPP 3DPP -2 17 DBREF 3DPP D -2 17 PDB 3DPP 3DPP -2 17 SEQRES 1 A 219 VAL LEU LEU LEU ASP VAL THR PRO LEU SER LEU GLY ILE SEQRES 2 A 219 GLU THR MET GLY GLY VAL MET THR THR LEU ILE ALA LYS SEQRES 3 A 219 ASN THR THR ILE PRO THR LYS HIS SER GLN VAL PHE SER SEQRES 4 A 219 THR ALA GLU ASP ASN GLN SER ALA VAL THR ILE HIS VAL SEQRES 5 A 219 LEU GLN GLY GLU ARG LYS ARG ALA ALA ASP ASN LYS SER SEQRES 6 A 219 LEU GLY GLN PHE ASN LEU ASP GLY ILE ASN PRO ALA PRO SEQRES 7 A 219 ARG GLY MET PRO GLN ILE GLU VAL THR PHE ASP ILE ASP SEQRES 8 A 219 ALA ASP GLY ILE LEU HIS VAL SER ALA LYS ASP LYS ASN SEQRES 9 A 219 SER GLY LYS GLU GLN LYS ILE THR ILE LYS ALA SER SER SEQRES 10 A 219 GLY LEU ASN GLU ASP GLU ILE GLN LYS MET VAL ARG ASP SEQRES 11 A 219 ALA GLU ALA ASN ALA GLU ALA ASP ARG LYS PHE GLU GLU SEQRES 12 A 219 LEU VAL GLN THR ARG ASN GLN GLY ASP HIS LEU LEU HIS SEQRES 13 A 219 SER THR ARG LYS GLN VAL GLU GLU ALA GLY ASP LYS LEU SEQRES 14 A 219 PRO ALA ASP ASP LYS THR ALA ILE GLU SER ALA LEU THR SEQRES 15 A 219 ALA LEU GLU THR ALA LEU LYS GLY GLU ASP LYS ALA ALA SEQRES 16 A 219 ILE GLU ALA LYS MET GLN GLU LEU ALA GLN VAL SER GLN SEQRES 17 A 219 LYS LEU MET GLU ILE ALA GLN GLN GLN HIS ALA SEQRES 1 B 219 VAL LEU LEU LEU ASP VAL THR PRO LEU SER LEU GLY ILE SEQRES 2 B 219 GLU THR MET GLY GLY VAL MET THR THR LEU ILE ALA LYS SEQRES 3 B 219 ASN THR THR ILE PRO THR LYS HIS SER GLN VAL PHE SER SEQRES 4 B 219 THR ALA GLU ASP ASN GLN SER ALA VAL THR ILE HIS VAL SEQRES 5 B 219 LEU GLN GLY GLU ARG LYS ARG ALA ALA ASP ASN LYS SER SEQRES 6 B 219 LEU GLY GLN PHE ASN LEU ASP GLY ILE ASN PRO ALA PRO SEQRES 7 B 219 ARG GLY MET PRO GLN ILE GLU VAL THR PHE ASP ILE ASP SEQRES 8 B 219 ALA ASP GLY ILE LEU HIS VAL SER ALA LYS ASP LYS ASN SEQRES 9 B 219 SER GLY LYS GLU GLN LYS ILE THR ILE LYS ALA SER SER SEQRES 10 B 219 GLY LEU ASN GLU ASP GLU ILE GLN LYS MET VAL ARG ASP SEQRES 11 B 219 ALA GLU ALA ASN ALA GLU ALA ASP ARG LYS PHE GLU GLU SEQRES 12 B 219 LEU VAL GLN THR ARG ASN GLN GLY ASP HIS LEU LEU HIS SEQRES 13 B 219 SER THR ARG LYS GLN VAL GLU GLU ALA GLY ASP LYS LEU SEQRES 14 B 219 PRO ALA ASP ASP LYS THR ALA ILE GLU SER ALA LEU THR SEQRES 15 B 219 ALA LEU GLU THR ALA LEU LYS GLY GLU ASP LYS ALA ALA SEQRES 16 B 219 ILE GLU ALA LYS MET GLN GLU LEU ALA GLN VAL SER GLN SEQRES 17 B 219 LYS LEU MET GLU ILE ALA GLN GLN GLN HIS ALA SEQRES 1 C 20 VAL ASP LYS LEU TYR ALC LEU PRO ARG PRO THR PRO PRO SEQRES 2 C 20 ARG PRO ILE TYR ASN ARG ASN SEQRES 1 D 20 VAL ASP LYS LEU TYR ALC LEU PRO ARG PRO THR PRO PRO SEQRES 2 D 20 ARG PRO ILE TYR ASN ARG ASN MODRES 3DPP ALC C 3 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID MODRES 3DPP ALC D 3 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID HET ALC C 3 11 HET ALC D 3 11 HET SO4 A1001 5 HETNAM ALC 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID HETNAM SO4 SULFATE ION FORMUL 3 ALC 2(C9 H17 N O2) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *309(H2 O) HELIX 1 1 ARG A 447 ASN A 451 5 5 HELIX 2 2 ASN A 508 ASN A 522 1 15 HELIX 3 3 ASN A 522 GLU A 551 1 30 HELIX 4 4 ALA A 559 SER A 567 1 9 HELIX 5 5 SER A 567 LEU A 576 1 10 HELIX 6 6 ASP A 580 VAL A 594 1 15 HELIX 7 7 ARG B 447 ASN B 451 5 5 HELIX 8 8 ASN B 508 ASN B 522 1 15 HELIX 9 9 ASN B 522 GLU B 552 1 31 HELIX 10 10 ALA B 553 LEU B 557 5 5 HELIX 11 11 PRO B 558 GLY B 578 1 21 HELIX 12 12 ASP B 580 VAL B 594 1 15 HELIX 13 13 SER B 595 ALA B 602 1 8 SHEET 1 A 2 VAL A 394 THR A 395 0 SHEET 2 A 2 THR A 416 THR A 417 -1 O THR A 416 N THR A 395 SHEET 1 B 4 VAL A 407 ILE A 412 0 SHEET 2 B 4 LEU A 399 THR A 403 -1 N LEU A 399 O ILE A 412 SHEET 3 B 4 VAL A 436 GLN A 442 -1 O LEU A 441 N GLY A 400 SHEET 4 B 4 LYS A 452 LEU A 459 -1 O LYS A 452 N GLN A 442 SHEET 1 C 5 GLU A 496 ILE A 501 0 SHEET 2 C 5 LEU A 484 ASP A 490 -1 N LEU A 484 O ILE A 501 SHEET 3 C 5 ILE A 472 ILE A 478 -1 N GLU A 473 O LYS A 489 SHEET 4 C 5 THR A 420 THR A 428 -1 N PHE A 426 O ILE A 472 SHEET 5 C 5 TYR D 2 LEU D 4 1 O TYR D 2 N SER A 427 SHEET 1 D 4 VAL B 407 ILE B 412 0 SHEET 2 D 4 LEU B 399 THR B 403 -1 N LEU B 399 O ILE B 412 SHEET 3 D 4 ALA B 435 GLN B 442 -1 O LEU B 441 N GLY B 400 SHEET 4 D 4 LYS B 452 ASP B 460 -1 O PHE B 457 N ILE B 438 SHEET 1 E 5 GLU B 496 ILE B 501 0 SHEET 2 E 5 LEU B 484 ASP B 490 -1 N VAL B 486 O ILE B 499 SHEET 3 E 5 ILE B 472 ILE B 478 -1 N ASP B 477 O HIS B 485 SHEET 4 E 5 THR B 420 THR B 428 -1 N PHE B 426 O ILE B 472 SHEET 5 E 5 ALC C 3 LEU C 4 1 O LEU C 4 N SER B 427 LINK C TYR C 2 N ALC C 3 1555 1555 1.18 LINK C ALC C 3 N LEU C 4 1555 1555 1.47 LINK C TYR D 2 N ALC D 3 1555 1555 1.32 LINK C ALC D 3 N LEU D 4 1555 1555 1.47 CISPEP 1 ILE A 418 PRO A 419 0 1.50 CISPEP 2 ILE B 418 PRO B 419 0 1.11 SITE 1 AC1 2 ARG A 517 ARG C 11 CRYST1 77.870 159.120 44.790 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012842 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022326 0.00000