HEADER CHAPERONE 29-JUN-17 5OBY TITLE MYCOPLASMA GENITALIUM DNAK-NBD IN COMPLEX WITH AMP-PNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAPERONE PROTEIN DNAK; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HSP70,HEAT SHOCK 70 KDA PROTEIN,HEAT SHOCK PROTEIN 70; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: CONTAINS A C-TERMINAL HEXA-HISTIDINE TAG. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOPLASMA GENITALIUM G37; SOURCE 3 ORGANISM_TAXID: 243273; SOURCE 4 GENE: DNAK, HSP70, MG305; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET21D KEYWDS COMPLEX, CO-FACTOR, ATP HYDROLYSIS, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR M.ADELL,B.CALISTO,I.FITA,L.MARTINELLI REVDAT 4 17-JAN-24 5OBY 1 LINK REVDAT 3 06-MAR-19 5OBY 1 REMARK REVDAT 2 03-OCT-18 5OBY 1 REMARK REVDAT 1 09-MAY-18 5OBY 0 JRNL AUTH M.ADELL,B.M.CALISTO,I.FITA,L.MARTINELLI JRNL TITL THE NUCLEOTIDE-BOUND/SUBSTRATE-BOUND CONFORMATION OF THE JRNL TITL 2 MYCOPLASMA GENITALIUM DNAK CHAPERONE. JRNL REF PROTEIN SCI. V. 27 1000 2018 JRNL REFN ESSN 1469-896X JRNL PMID 29520883 JRNL DOI 10.1002/PRO.3401 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 78.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 121266 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 6297 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8459 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 438 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2765 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 315 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48000 REMARK 3 B22 (A**2) : 0.48000 REMARK 3 B33 (A**2) : -1.54000 REMARK 3 B12 (A**2) : 0.24000 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): 0.035 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.035 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.596 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2930 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2859 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3976 ; 2.132 ; 2.010 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6660 ; 2.326 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 382 ; 4.931 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;36.862 ;25.345 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 546 ;12.894 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;13.380 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 471 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3212 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 514 ; 0.008 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 5789 ;10.811 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 197 ;31.934 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5871 ;21.546 ; 5.000 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.30 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5OBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9495 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL-CUT REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 127585 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 78.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.50000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 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: PHASER REMARK 200 STARTING MODEL: 5OBW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, AMMONIUM SULFATE, POTASSIUM REMARK 280 THIOCYANATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 78.53250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.34076 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.92733 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 78.53250 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 45.34076 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.92733 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 78.53250 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 45.34076 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 18.92733 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 90.68152 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 37.85467 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 90.68152 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 37.85467 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 90.68152 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 37.85467 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL 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 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 HIS A 369 REMARK 465 HIS A 370 REMARK 465 HIS A 371 REMARK 465 HIS A 372 REMARK 465 HIS A 373 REMARK 465 HIS A 374 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 ASP A 4 CG OD1 OD2 REMARK 470 MET A 237 CG SD CE REMARK 470 GLU A 368 CG CD OE1 OE2 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 O3 SO4 A 407 O HOH A 501 1.61 REMARK 500 O ASN A 48 O HOH A 502 1.79 REMARK 500 O HOH A 510 O HOH A 766 1.94 REMARK 500 O HOH A 505 O HOH A 642 1.98 REMARK 500 O HOH A 503 O HOH A 796 2.03 REMARK 500 O HOH A 511 O HOH A 580 2.04 REMARK 500 O HOH A 644 O HOH A 781 2.05 REMARK 500 NZ LYS A 91 O HOH A 502 2.18 REMARK 500 O HOH A 749 O HOH A 794 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 GLU A 170 CD GLU A 170 OE1 0.074 REMARK 500 GLU A 170 CD GLU A 170 OE2 0.092 REMARK 500 SER A 220 CB SER A 220 OG -0.083 REMARK 500 SER A 301 CB SER A 301 OG -0.097 REMARK 500 GLU A 312 CD GLU A 312 OE1 0.123 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 MET A 23 CG - SD - CE ANGL. DEV. = -11.9 DEGREES REMARK 500 ARG A 59 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 MET A 61 CG - SD - CE ANGL. DEV. = -10.3 DEGREES REMARK 500 ASN A 153 CB - CA - C ANGL. DEV. = 14.4 DEGREES REMARK 500 ARG A 248 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 248 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 LEU A 278 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 ARG A 297 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 297 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 325 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 349 CB - CG - OD1 ANGL. DEV. = 5.8 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 ASN A 48 -120.53 54.67 REMARK 500 ARG A 344 19.55 -142.07 REMARK 500 ASN A 347 117.96 -39.04 REMARK 500 ASP A 366 101.39 81.11 REMARK 500 LEU A 367 43.99 -89.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 134 0.09 SIDE CHAIN 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 A 813 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A 814 DISTANCE = 7.56 ANGSTROMS REMARK 525 HOH A 815 DISTANCE = 7.65 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 A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ANP A 402 O1B REMARK 620 2 HOH A 549 O 158.8 REMARK 620 3 HOH A 580 O 78.9 85.1 REMARK 620 4 HOH A 593 O 91.8 99.7 81.9 REMARK 620 5 HOH A 652 O 79.9 87.0 92.3 170.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ANP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 408 DBREF 5OBY A 1 366 UNP P47547 DNAK_MYCGE 1 366 SEQADV 5OBY LEU A 367 UNP P47547 EXPRESSION TAG SEQADV 5OBY GLU A 368 UNP P47547 EXPRESSION TAG SEQADV 5OBY HIS A 369 UNP P47547 EXPRESSION TAG SEQADV 5OBY HIS A 370 UNP P47547 EXPRESSION TAG SEQADV 5OBY HIS A 371 UNP P47547 EXPRESSION TAG SEQADV 5OBY HIS A 372 UNP P47547 EXPRESSION TAG SEQADV 5OBY HIS A 373 UNP P47547 EXPRESSION TAG SEQADV 5OBY HIS A 374 UNP P47547 EXPRESSION TAG SEQRES 1 A 374 MET SER ALA ASP ASN GLY LEU ILE ILE GLY ILE ASP LEU SEQRES 2 A 374 GLY THR THR ASN SER CYS VAL SER VAL MET GLU GLY GLY SEQRES 3 A 374 ARG PRO VAL VAL LEU GLU ASN PRO GLU GLY LYS ARG THR SEQRES 4 A 374 THR PRO SER ILE VAL SER TYR LYS ASN ASN GLU ILE ILE SEQRES 5 A 374 VAL GLY ASP ALA ALA LYS ARG GLN MET VAL THR ASN PRO SEQRES 6 A 374 ASN THR ILE VAL SER ILE LYS ARG LEU MET GLY THR SER SEQRES 7 A 374 ASN LYS VAL LYS VAL GLN ASN ALA ASP GLY THR THR LYS SEQRES 8 A 374 GLU LEU SER PRO GLU GLN VAL SER ALA GLN ILE LEU SER SEQRES 9 A 374 TYR LEU LYS ASP PHE ALA GLU LYS LYS ILE GLY LYS LYS SEQRES 10 A 374 ILE SER ARG ALA VAL ILE THR VAL PRO ALA TYR PHE ASN SEQRES 11 A 374 ASP ALA GLU ARG ASN ALA THR LYS THR ALA GLY LYS ILE SEQRES 12 A 374 ALA GLY LEU ASN VAL GLU ARG ILE ILE ASN GLU PRO THR SEQRES 13 A 374 ALA ALA ALA LEU ALA TYR GLY ILE ASP LYS ALA SER ARG SEQRES 14 A 374 GLU MET LYS VAL LEU VAL TYR ASP LEU GLY GLY GLY THR SEQRES 15 A 374 PHE ASP VAL SER LEU LEU ASP ILE ALA GLU GLY THR PHE SEQRES 16 A 374 GLU VAL LEU ALA THR ALA GLY ASP ASN ARG LEU GLY GLY SEQRES 17 A 374 ASP ASP TRP ASP ASN LYS ILE ILE GLU TYR ILE SER ALA SEQRES 18 A 374 TYR ILE ALA LYS GLU HIS GLN GLY LEU ASN LEU SER LYS SEQRES 19 A 374 ASP LYS MET ALA MET GLN ARG LEU LYS GLU ALA ALA GLU SEQRES 20 A 374 ARG ALA LYS ILE GLU LEU SER ALA GLN LEU GLU THR ILE SEQRES 21 A 374 ILE SER LEU PRO PHE LEU THR VAL THR GLN LYS GLY PRO SEQRES 22 A 374 VAL ASN VAL GLU LEU LYS LEU THR ARG ALA LYS PHE GLU SEQRES 23 A 374 GLU LEU THR LYS PRO LEU LEU GLU ARG THR ARG ASN PRO SEQRES 24 A 374 ILE SER ASP VAL ILE LYS GLU ALA LYS ILE LYS PRO GLU SEQRES 25 A 374 GLU ILE ASN GLU ILE LEU LEU VAL GLY GLY SER THR ARG SEQRES 26 A 374 MET PRO ALA VAL GLN LYS LEU VAL GLU SER MET VAL PRO SEQRES 27 A 374 GLY LYS LYS PRO ASN ARG SER ILE ASN PRO ASP GLU VAL SEQRES 28 A 374 VAL ALA ILE GLY ALA ALA ILE GLN GLY GLY VAL LEU ARG SEQRES 29 A 374 GLY ASP LEU GLU HIS HIS HIS HIS HIS HIS HET MG A 401 1 HET ANP A 402 31 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HETNAM MG MAGNESIUM ION HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG MG 2+ FORMUL 3 ANP C10 H17 N6 O12 P3 FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 SO4 3(O4 S 2-) FORMUL 10 HOH *315(H2 O) HELIX 1 AA1 GLY A 54 ARG A 59 1 6 HELIX 2 AA2 SER A 70 MET A 75 5 6 HELIX 3 AA3 SER A 94 GLY A 115 1 22 HELIX 4 AA4 ASN A 130 ALA A 144 1 15 HELIX 5 AA5 GLU A 154 TYR A 162 1 9 HELIX 6 AA6 GLY A 163 ALA A 167 5 5 HELIX 7 AA7 GLY A 207 HIS A 227 1 21 HELIX 8 AA8 ASN A 231 LYS A 234 5 4 HELIX 9 AA9 ASP A 235 GLN A 256 1 22 HELIX 10 AB1 ARG A 282 THR A 289 1 8 HELIX 11 AB2 THR A 289 THR A 296 1 8 HELIX 12 AB3 THR A 296 LYS A 308 1 13 HELIX 13 AB4 LYS A 310 ILE A 314 5 5 HELIX 14 AB5 GLY A 321 ARG A 325 5 5 HELIX 15 AB6 MET A 326 VAL A 337 1 12 HELIX 16 AB7 GLU A 350 GLY A 365 1 16 SHEET 1 AA1 3 ARG A 27 VAL A 30 0 SHEET 2 AA1 3 ASN A 17 GLU A 24 -1 N GLU A 24 O ARG A 27 SHEET 3 AA1 3 THR A 40 PRO A 41 -1 O THR A 40 N SER A 18 SHEET 1 AA2 5 ARG A 27 VAL A 30 0 SHEET 2 AA2 5 ASN A 17 GLU A 24 -1 N GLU A 24 O ARG A 27 SHEET 3 AA2 5 ILE A 9 LEU A 13 -1 N GLY A 10 O SER A 21 SHEET 4 AA2 5 ARG A 120 VAL A 125 1 O VAL A 122 N ILE A 9 SHEET 5 AA2 5 ASN A 147 ASN A 153 1 O ASN A 147 N ALA A 121 SHEET 1 AA3 3 GLU A 50 VAL A 53 0 SHEET 2 AA3 3 VAL A 44 LYS A 47 -1 N SER A 45 O ILE A 52 SHEET 3 AA3 3 THR A 67 ILE A 68 -1 O ILE A 68 N VAL A 44 SHEET 1 AA4 2 VAL A 81 GLN A 84 0 SHEET 2 AA4 2 THR A 90 LEU A 93 -1 O LYS A 91 N VAL A 83 SHEET 1 AA5 4 THR A 194 ASP A 203 0 SHEET 2 AA5 4 PHE A 183 ALA A 191 -1 N VAL A 185 O ALA A 201 SHEET 3 AA5 4 MET A 171 LEU A 178 -1 N VAL A 175 O SER A 186 SHEET 4 AA5 4 GLU A 316 VAL A 320 1 O LEU A 318 N LEU A 174 SHEET 1 AA6 2 GLU A 258 THR A 269 0 SHEET 2 AA6 2 GLY A 272 THR A 281 -1 O LEU A 278 N ILE A 261 LINK MG MG A 401 O1B ANP A 402 1555 1555 2.49 LINK MG MG A 401 O HOH A 549 1555 1555 2.35 LINK MG MG A 401 O HOH A 580 1555 1555 2.42 LINK MG MG A 401 O HOH A 593 1555 1555 1.91 LINK MG MG A 401 O HOH A 652 1555 1555 1.84 SITE 1 AC1 5 ANP A 402 HOH A 549 HOH A 580 HOH A 593 SITE 2 AC1 5 HOH A 652 SITE 1 AC2 30 GLY A 14 THR A 15 THR A 16 ASN A 17 SITE 2 AC2 30 GLY A 179 GLY A 180 GLY A 181 THR A 182 SITE 3 AC2 30 GLY A 208 GLU A 247 LYS A 250 SER A 254 SITE 4 AC2 30 GLY A 321 GLY A 322 SER A 323 ARG A 325 SITE 5 AC2 30 MET A 326 MG A 401 GOL A 403 HOH A 504 SITE 6 AC2 30 HOH A 509 HOH A 511 HOH A 526 HOH A 593 SITE 7 AC2 30 HOH A 596 HOH A 601 HOH A 622 HOH A 652 SITE 8 AC2 30 HOH A 685 HOH A 701 SITE 1 AC3 9 ASN A 17 LYS A 58 GLU A 247 ASP A 349 SITE 2 AC3 9 ANP A 402 HOH A 504 HOH A 505 HOH A 507 SITE 3 AC3 9 HOH A 555 SITE 1 AC4 8 THR A 15 LYS A 72 ARG A 73 TYR A 128 SITE 2 AC4 8 PHE A 129 THR A 182 ASN A 204 HOH A 508 SITE 1 AC5 5 ARG A 150 ARG A 169 ASN A 315 HOH A 713 SITE 2 AC5 5 HOH A 733 SITE 1 AC6 4 VAL A 29 VAL A 30 ARG A 38 HOH A 605 SITE 1 AC7 4 LYS A 138 ARG A 150 ILE A 151 HOH A 501 SITE 1 AC8 3 ARG A 295 HOH A 514 HOH A 562 CRYST1 157.065 157.065 56.782 90.00 90.00 120.00 H 3 9 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 0.006367 0.003676 0.000000 0.00000 SCALE2 0.000000 0.007352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017611 0.00000