HEADER CHAPERONE 02-AUG-07 2V7Y TITLE CRYSTAL STRUCTURE OF THE MOLECULAR CHAPERONE DNAK FROM GEOBACILLUS TITLE 2 KAUSTOPHILUS HTA426 IN POST-ATP HYDROLYSIS STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAPERONE PROTEIN DNAK; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUCLEOTIDE-BINDING DOMAIN AND SUBSTRATE-BINDING DOMAIN COMPND 5 (RESIDUES 1-509); COMPND 6 SYNONYM: HEAT SHOCK PROTEIN 70, HSP70; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS HTA426; SOURCE 3 ORGANISM_TAXID: 235909; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET21A KEYWDS HSP70, DNAK, CHAPERONE, HEAT SHOCK PROTEIN, ATPASE, DOMAIN KEYWDS 2 REARRANGEMENT EXPDTA X-RAY DIFFRACTION AUTHOR Y.-W.CHANG,Y.-J.SUN,C.WANG,C.-D.HSIAO REVDAT 3 13-DEC-23 2V7Y 1 LINK REVDAT 2 24-FEB-09 2V7Y 1 VERSN REVDAT 1 08-APR-08 2V7Y 0 JRNL AUTH Y.-W.CHANG,Y.-J.SUN,C.WANG,C.-D.HSIAO JRNL TITL CRYSTAL STRUCTURES OF THE 70-KDA HEAT SHOCK PROTEINS IN JRNL TITL 2 DOMAIN DISJOINING CONFORMATION. JRNL REF J.BIOL.CHEM. V. 283 15502 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18400763 JRNL DOI 10.1074/JBC.M708992200 REMARK 2 REMARK 2 RESOLUTION. 2.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 259880.480 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 25994 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) : 0.227 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1251 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.52 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3708 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE : 0.3860 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 198 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3720 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.78000 REMARK 3 B22 (A**2) : 5.04000 REMARK 3 B33 (A**2) : -1.26000 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.34 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 2.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 4.220 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.170 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.560 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.430 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.860 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 50.39 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : ADP.PAR REMARK 3 PARAMETER FILE 5 : PO4.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : ADP.TOP REMARK 3 TOPOLOGY FILE 5 : PO4.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED. RESIDUES REMARK 3 GLU46, GLU216, ARG436, LYS464, LYS471, SER472, SER473, SER474, REMARK 3 LUE476, GLU478, GLU479, GLU480, ILU481, ARG483, MET484, ILU485, REMARK 3 LYS486, GLU487, GLU490, ASN491, GLU493, ASP495, ARG496, LYS497, REMARK 3 ARG498, LYS499, GLU500, GLU503, LEU504 FOR WHICH SIDE CHAIN REMARK 3 ELECTRON DENSITY WAS POOR WERE MODELED AS ALANINES. RESIDUES 505- REMARK 3 509 ARE DISORDERED. REMARK 4 REMARK 4 2V7Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1290033337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : LN2-COOLED, FIXED-EXIT DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : VERTICALLY COLLIMATING REMARK 200 PREMIRROR, LN2-COOLED FIXED-EXIT REMARK 200 DOUBLE CRYSTAL SI(111) REMARK 200 MONOCHROMATOR , TOROIDAL REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BLU-ICE CONTROL SOFTWARE REMARK 200 DATA SCALING SOFTWARE : SCALEPACK HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25994 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 29.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: PDB ENTRY 3HSC, 1DKZ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM AMMONIUM CITRATE, PH 7.5, 20% REMARK 280 (V/V) ISOPROPANOL, 15% (W/V) PEG3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 26.37650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 91.93200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.72750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 91.93200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.37650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.72750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 ARG A 505 REMARK 465 ASN A 506 REMARK 465 GLU A 507 REMARK 465 ALA A 508 REMARK 465 ASP A 509 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 46 CG CD OE1 OE2 REMARK 470 GLU A 216 CG CD OE1 OE2 REMARK 470 ARG A 436 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 464 CG CD CE NZ REMARK 470 LYS A 471 CG CD CE NZ REMARK 470 SER A 472 OG REMARK 470 SER A 473 OG REMARK 470 SER A 474 OG REMARK 470 LEU A 476 CG CD1 CD2 REMARK 470 GLU A 478 CG CD OE1 OE2 REMARK 470 GLU A 479 CG CD OE1 OE2 REMARK 470 GLU A 480 CG CD OE1 OE2 REMARK 470 ILE A 481 CG1 CG2 CD1 REMARK 470 ARG A 483 CG CD NE CZ NH1 NH2 REMARK 470 MET A 484 CG SD CE REMARK 470 ILE A 485 CG1 CG2 CD1 REMARK 470 LYS A 486 CG CD CE NZ REMARK 470 GLU A 487 CG CD OE1 OE2 REMARK 470 GLU A 490 CG CD OE1 OE2 REMARK 470 ASN A 491 CG OD1 ND2 REMARK 470 GLU A 493 CG CD OE1 OE2 REMARK 470 ASP A 495 CG OD1 OD2 REMARK 470 ARG A 496 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 497 CG CD CE NZ REMARK 470 ARG A 498 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 499 CG CD CE NZ REMARK 470 GLU A 500 CG CD OE1 OE2 REMARK 470 GLU A 503 CG CD OE1 OE2 REMARK 470 LEU A 504 CG CD1 CD2 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 CA SER A 472 CB SER A 474 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 43 C ASN A 44 N 0.159 REMARK 500 PHE A 201 C ASP A 202 N -0.187 REMARK 500 VAL A 204 C ILE A 205 N -0.176 REMARK 500 ALA A 399 C ASP A 400 N -0.223 REMARK 500 ALA A 492 C GLU A 493 N 0.200 REMARK 500 GLU A 503 C LEU A 504 N -0.139 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 ASN A 44 C - N - CA ANGL. DEV. = -22.8 DEGREES REMARK 500 ASN A 44 CA - C - O ANGL. DEV. = 18.8 DEGREES REMARK 500 ASN A 44 CA - C - N ANGL. DEV. = -21.4 DEGREES REMARK 500 ARG A 47 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 47 O - C - N ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 TYR A 96 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 125 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES REMARK 500 ASP A 202 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 VAL A 204 CA - CB - CG2 ANGL. DEV. = 9.8 DEGREES REMARK 500 VAL A 204 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 ASP A 400 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 THR A 469 CA - CB - OG1 ANGL. DEV. = 12.7 DEGREES REMARK 500 ILE A 470 CA - C - N ANGL. DEV. = -16.1 DEGREES REMARK 500 LYS A 471 C - N - CA ANGL. DEV. = -18.1 DEGREES REMARK 500 SER A 473 C - N - CA ANGL. DEV. = 22.2 DEGREES REMARK 500 SER A 473 CA - C - N ANGL. DEV. = -15.7 DEGREES REMARK 500 SER A 473 O - C - N ANGL. DEV. = 9.8 DEGREES REMARK 500 SER A 474 C - N - CA ANGL. DEV. = 22.3 DEGREES REMARK 500 SER A 474 CA - C - N ANGL. DEV. = -15.5 DEGREES REMARK 500 LEU A 476 C - N - CA ANGL. DEV. = -15.5 DEGREES REMARK 500 GLN A 482 CB - CA - C ANGL. DEV. = 20.0 DEGREES REMARK 500 GLU A 493 C - N - CA ANGL. DEV. = -22.2 DEGREES REMARK 500 GLU A 493 O - C - N ANGL. DEV. = -9.9 DEGREES REMARK 500 ASP A 495 C - N - CA ANGL. DEV. = 20.5 DEGREES REMARK 500 LYS A 497 C - N - CA ANGL. DEV. = 16.0 DEGREES REMARK 500 GLU A 503 C - N - CA ANGL. DEV. = 25.8 DEGREES REMARK 500 LEU A 504 C - N - CA ANGL. DEV. = 17.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 2 158.35 -43.59 REMARK 500 MET A 71 131.71 -37.84 REMARK 500 HIS A 195 44.78 -143.17 REMARK 500 HIS A 217 -6.74 -141.47 REMARK 500 SER A 222 0.87 -64.95 REMARK 500 SER A 256 -157.41 -148.49 REMARK 500 ALA A 257 145.00 -170.10 REMARK 500 ASN A 258 -158.67 -129.89 REMARK 500 MET A 267 142.99 -175.10 REMARK 500 ASN A 335 110.67 -38.24 REMARK 500 MET A 373 124.58 -29.04 REMARK 500 ASN A 384 38.42 70.42 REMARK 500 ASN A 401 6.96 86.16 REMARK 500 SER A 477 -87.31 -129.71 REMARK 500 GLU A 478 -71.54 -85.49 REMARK 500 GLU A 490 -79.01 -32.21 REMARK 500 ARG A 496 -35.19 -37.89 REMARK 500 LYS A 497 -21.11 -30.24 REMARK 500 GLU A 500 3.64 -57.75 REMARK 500 ALA A 501 46.88 -82.94 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 ILE A 470 LYS A 471 -140.57 REMARK 500 SER A 472 SER A 473 -118.89 REMARK 500 SER A 473 SER A 474 -136.41 REMARK 500 ALA A 492 GLU A 493 -145.19 REMARK 500 GLU A 493 ALA A 494 136.88 REMARK 500 ALA A 494 ASP A 495 130.30 REMARK 500 ASP A 495 ARG A 496 138.43 REMARK 500 GLU A 503 LEU A 504 -82.63 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 ASN A 44 -13.04 REMARK 500 ARG A 47 13.53 REMARK 500 ARG A 125 12.41 REMARK 500 VAL A 204 11.62 REMARK 500 SER A 472 -15.74 REMARK 500 SER A 474 -10.84 REMARK 500 GLY A 475 -10.09 REMARK 500 ALA A 492 16.75 REMARK 500 GLU A 493 -26.86 REMARK 500 ALA A 494 -11.95 REMARK 500 ASP A 495 -20.66 REMARK 500 ARG A 498 -21.55 REMARK 500 GLU A 503 -13.33 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 A2012 DISTANCE = 7.53 ANGSTROMS REMARK 525 HOH A2028 DISTANCE = 6.92 ANGSTROMS REMARK 525 HOH A2091 DISTANCE = 5.99 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 MG A1507 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A1505 O3B REMARK 620 2 PO4 A1506 O2 80.9 REMARK 620 N 1 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A1505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1507 DBREF 2V7Y A 1 509 UNP Q5KWZ7 DNAK_GEOKA 1 509 SEQRES 1 A 509 MET SER LYS ILE ILE GLY ILE ASP LEU GLY THR THR ASN SEQRES 2 A 509 SER CYS VAL ALA VAL LEU GLU GLY GLY GLU VAL LYS VAL SEQRES 3 A 509 ILE PRO ASN PRO GLU GLY ASN ARG THR THR PRO SER VAL SEQRES 4 A 509 VAL ALA PHE LYS ASN GLY GLU ARG LEU VAL GLY GLU VAL SEQRES 5 A 509 ALA LYS ARG GLN ALA ILE THR ASN PRO ASN THR ILE ILE SEQRES 6 A 509 SER ILE LYS ARG HIS MET GLY THR ASP TYR LYS VAL GLU SEQRES 7 A 509 ILE GLU GLY LYS GLN TYR THR PRO GLN GLU ILE SER ALA SEQRES 8 A 509 ILE ILE LEU GLN TYR LEU LYS SER TYR ALA GLU ASP TYR SEQRES 9 A 509 LEU GLY GLU PRO VAL THR ARG ALA VAL ILE THR VAL PRO SEQRES 10 A 509 ALA TYR PHE ASN ASP ALA GLN ARG GLN ALA THR LYS ASP SEQRES 11 A 509 ALA GLY ARG ILE ALA GLY LEU GLU VAL GLU ARG ILE ILE SEQRES 12 A 509 ASN GLU PRO THR ALA ALA ALA LEU ALA TYR GLY LEU ASP SEQRES 13 A 509 LYS GLU GLU ASP GLN THR ILE LEU VAL TYR ASP LEU GLY SEQRES 14 A 509 GLY GLY THR PHE ASP VAL SER ILE LEU GLU LEU GLY ASP SEQRES 15 A 509 GLY VAL PHE GLU VAL LYS ALA THR ALA GLY ASP ASN HIS SEQRES 16 A 509 LEU GLY GLY ASP ASP PHE ASP GLN VAL ILE ILE ASP TYR SEQRES 17 A 509 LEU VAL ASN GLN PHE LYS GLN GLU HIS GLY ILE ASP LEU SEQRES 18 A 509 SER LYS ASP LYS MET ALA LEU GLN ARG LEU LYS ASP ALA SEQRES 19 A 509 ALA GLU LYS ALA LYS LYS GLU LEU SER GLY VAL THR GLN SEQRES 20 A 509 THR GLN ILE SER LEU PRO PHE ILE SER ALA ASN GLU ASN SEQRES 21 A 509 GLY PRO LEU HIS LEU GLU MET THR LEU THR ARG ALA LYS SEQRES 22 A 509 PHE GLU GLU LEU SER ALA HIS LEU VAL GLU ARG THR MET SEQRES 23 A 509 GLY PRO VAL ARG GLN ALA LEU GLN ASP ALA GLY LEU THR SEQRES 24 A 509 PRO ALA ASP ILE ASP LYS VAL ILE LEU VAL GLY GLY SER SEQRES 25 A 509 THR ARG ILE PRO ALA VAL GLN GLU ALA ILE LYS ARG GLU SEQRES 26 A 509 LEU GLY LYS GLU PRO HIS LYS GLY VAL ASN PRO ASP GLU SEQRES 27 A 509 VAL VAL ALA ILE GLY ALA ALA ILE GLN GLY GLY VAL ILE SEQRES 28 A 509 ALA GLY GLU VAL LYS ASP VAL VAL LEU LEU ASP VAL THR SEQRES 29 A 509 PRO LEU SER LEU GLY ILE GLU THR MET GLY GLY VAL PHE SEQRES 30 A 509 THR LYS LEU ILE GLU ARG ASN THR THR ILE PRO THR SER SEQRES 31 A 509 LYS SER GLN VAL PHE THR THR ALA ALA ASP ASN GLN THR SEQRES 32 A 509 THR VAL ASP ILE HIS VAL LEU GLN GLY GLU ARG PRO MET SEQRES 33 A 509 ALA ALA ASP ASN LYS SER LEU GLY ARG PHE GLN LEU THR SEQRES 34 A 509 GLY ILE PRO PRO ALA PRO ARG GLY VAL PRO GLN ILE GLU SEQRES 35 A 509 VAL THR PHE ASP ILE ASP ALA ASN GLY ILE VAL HIS VAL SEQRES 36 A 509 ARG ALA LYS ASP LEU GLY THR ASN LYS GLU GLN SER ILE SEQRES 37 A 509 THR ILE LYS SER SER SER GLY LEU SER GLU GLU GLU ILE SEQRES 38 A 509 GLN ARG MET ILE LYS GLU ALA GLU GLU ASN ALA GLU ALA SEQRES 39 A 509 ASP ARG LYS ARG LYS GLU ALA ALA GLU LEU ARG ASN GLU SEQRES 40 A 509 ALA ASP HET ADP A1505 27 HET PO4 A1506 5 HET MG A1507 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 PO4 O4 P 3- FORMUL 4 MG MG 2+ FORMUL 5 HOH *166(H2 O) HELIX 1 1 GLY A 50 ARG A 55 1 6 HELIX 2 2 ILE A 67 HIS A 70 5 4 HELIX 3 3 THR A 85 GLY A 106 1 22 HELIX 4 4 ASN A 121 ALA A 135 1 15 HELIX 5 5 GLU A 145 TYR A 153 1 9 HELIX 6 6 GLY A 154 GLU A 158 5 5 HELIX 7 7 GLY A 197 GLY A 218 1 22 HELIX 8 8 ASP A 220 LYS A 223 5 4 HELIX 9 9 ASP A 224 LEU A 242 1 19 HELIX 10 10 ARG A 271 SER A 278 1 8 HELIX 11 11 SER A 278 ARG A 284 1 7 HELIX 12 12 THR A 285 GLY A 297 1 13 HELIX 13 13 THR A 299 ILE A 303 5 5 HELIX 14 14 GLY A 310 ARG A 314 5 5 HELIX 15 15 ILE A 315 GLY A 327 1 13 HELIX 16 16 GLU A 338 GLY A 353 1 16 HELIX 17 17 ALA A 417 ASN A 420 5 4 HELIX 18 18 GLU A 478 ASN A 491 1 14 HELIX 19 19 GLU A 493 ALA A 501 5 9 SHEET 1 AA 5 GLU A 23 VAL A 26 0 SHEET 2 AA 5 ASN A 13 GLU A 20 -1 O VAL A 18 N LYS A 25 SHEET 3 AA 5 ILE A 4 LEU A 9 -1 O GLY A 6 N ALA A 17 SHEET 4 AA 5 ARG A 111 VAL A 116 1 O ARG A 111 N ILE A 5 SHEET 5 AA 5 GLU A 138 ASN A 144 1 O GLU A 138 N ALA A 112 SHEET 1 AB 3 GLU A 23 VAL A 26 0 SHEET 2 AB 3 ASN A 13 GLU A 20 -1 O VAL A 18 N LYS A 25 SHEET 3 AB 3 THR A 36 PRO A 37 -1 O THR A 36 N SER A 14 SHEET 1 AC 3 ARG A 47 VAL A 49 0 SHEET 2 AC 3 VAL A 39 PHE A 42 -1 O ALA A 41 N LEU A 48 SHEET 3 AC 3 THR A 63 ILE A 65 -1 O ILE A 64 N VAL A 40 SHEET 1 AD 2 VAL A 77 ILE A 79 0 SHEET 2 AD 2 LYS A 82 TYR A 84 -1 O LYS A 82 N ILE A 79 SHEET 1 AE 4 VAL A 184 ASP A 193 0 SHEET 2 AE 4 PHE A 173 GLY A 181 -1 O PHE A 173 N ASP A 193 SHEET 3 AE 4 GLN A 161 LEU A 168 -1 O GLN A 161 N LEU A 180 SHEET 4 AE 4 LYS A 305 VAL A 309 1 O LYS A 305 N LEU A 164 SHEET 1 AF 2 GLN A 247 ASN A 258 0 SHEET 2 AF 2 GLY A 261 THR A 270 -1 O GLY A 261 N ASN A 258 SHEET 1 AG 4 VAL A 376 ILE A 381 0 SHEET 2 AG 4 SER A 367 THR A 372 -1 O LEU A 368 N LEU A 380 SHEET 3 AG 4 THR A 404 GLY A 412 -1 O HIS A 408 N GLU A 371 SHEET 4 AG 4 LYS A 421 THR A 429 -1 O LYS A 421 N GLN A 411 SHEET 1 AH 4 THR A 389 PHE A 395 0 SHEET 2 AH 4 ILE A 441 ILE A 447 -1 O ILE A 441 N PHE A 395 SHEET 3 AH 4 VAL A 453 ASP A 459 -1 O HIS A 454 N ASP A 446 SHEET 4 AH 4 GLU A 465 ILE A 470 -1 O GLN A 466 N ALA A 457 LINK O3B ADP A1505 MG MG A1507 1555 1555 2.52 LINK O2 PO4 A1506 MG MG A1507 1555 1555 2.54 CISPEP 1 ILE A 387 PRO A 388 0 0.11 SITE 1 AC1 20 GLY A 10 THR A 11 THR A 12 ASN A 13 SITE 2 AC1 20 GLY A 169 GLY A 170 GLY A 198 GLU A 236 SITE 3 AC1 20 LYS A 239 LYS A 240 SER A 243 GLY A 310 SITE 4 AC1 20 GLY A 311 SER A 312 ARG A 314 ILE A 315 SITE 5 AC1 20 PO4 A1506 MG A1507 HOH A2127 HOH A2166 SITE 1 AC2 8 GLY A 10 THR A 11 LYS A 68 GLU A 145 SITE 2 AC2 8 THR A 172 ADP A1505 MG A1507 HOH A2089 SITE 1 AC3 2 ADP A1505 PO4 A1506 CRYST1 52.753 71.455 183.864 90.00 90.00 90.00 P 21 21 21 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 0.018956 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013995 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005439 0.00000