HEADER DNA BINDING PROTEIN 18-NOV-19 6TGT TITLE THE CALCIUM SOAKED CRYSTAL STRUCTURE OF THE DPS2 FROM DEINOCOCCUS TITLE 2 RADIODURANS TO 2.16A RESOLUTION (SOAKED IN CACL2 [5MM] FOR 20 MIN). COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PROTECTION DURING STARVATION PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 EC: 1.16.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS (STRAIN ATCC 13939 / SOURCE 3 DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / SOURCE 4 VKM B-1422); SOURCE 5 ORGANISM_TAXID: 243230; SOURCE 6 STRAIN: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / SOURCE 7 NCIMB 9279 / R1 / VKM B-1422; SOURCE 8 GENE: DPS2, DPS-2, DR_B0092; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: DE3; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PDEST14 KEYWDS IRON BIOMINERALISATION, IRON STORAGE, IRON DETOXIFICATION, DNA KEYWDS 2 BINDING, CALCIUM BINDING, METALLOPROTEIN., DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.G.CUYPERS,C.V.ROMAO,E.P.MITCHELL,S.MCSWEENEY REVDAT 2 24-JAN-24 6TGT 1 REMARK REVDAT 1 02-DEC-20 6TGT 0 JRNL AUTH M.G.CUYPERS,S.MCSWEENEY,C.V.ROMAO,E.P.MITCHELL JRNL TITL THE CALCIUM SOAKED CRYSTAL STRUCTURE OF THE DPS2 FROM JRNL TITL 2 DEINOCOCCUS RADIODURANS TO 2.16A RESOLUTION (SOAKED IN CACL2 JRNL TITL 3 [5MM] FOR 20 MIN). JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 12087 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 587 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 867 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3430 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1284 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.177 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.000 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.004 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 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 : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6TGT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105445. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-05 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 : 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) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12682 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.155 REMARK 200 RESOLUTION RANGE LOW (A) : 51.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 1.44100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 2C2J REMARK 200 REMARK 200 REMARK: CUBE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M KCL, 0.01 M MGCL2, 0.05 M HEPES REMARK 280 PH 7.0, 5% V/V PEG 400 (HAMPTON NATRIX CRYSTAL SCREEN # 35), PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 3 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 55290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1189.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 8 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT1 9 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 9 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 11 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 12 1.000000 0.000000 0.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CA CA A 304 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 434 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 463 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 510 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 1 REMARK 465 GLY A 2 REMARK 465 VAL A 3 REMARK 465 PRO A 4 REMARK 465 SER A 5 REMARK 465 THR A 6 REMARK 465 ASN A 7 REMARK 465 VAL A 8 REMARK 465 ASN A 9 REMARK 465 THR A 10 REMARK 465 PRO A 11 REMARK 465 ALA A 12 REMARK 465 PRO A 13 REMARK 465 ASN A 14 REMARK 465 THR A 15 REMARK 465 GLY A 16 REMARK 465 GLN A 17 REMARK 465 SER A 18 REMARK 465 THR A 19 REMARK 465 ALA A 20 REMARK 465 GLN A 21 REMARK 465 ASN A 22 REMARK 465 THR A 23 REMARK 465 ASN A 24 REMARK 465 THR A 25 REMARK 465 ALA A 26 REMARK 465 SER A 27 REMARK 465 PRO A 28 REMARK 465 LEU A 29 REMARK 465 PRO A 30 REMARK 465 TYR A 31 REMARK 465 ASN A 32 REMARK 465 ARG A 33 REMARK 465 ALA A 34 REMARK 465 THR A 35 REMARK 465 THR A 36 REMARK 465 LEU A 37 REMARK 465 PRO A 38 REMARK 465 ALA A 39 REMARK 465 ALA A 40 REMARK 465 GLY A 41 REMARK 465 THR A 42 REMARK 465 GLU A 43 REMARK 465 PRO A 207 REMARK 465 LEU A 208 REMARK 465 ARG A 209 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 46 CG CD CE NZ REMARK 470 ARG A 122 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 159 CD OE1 OE2 REMARK 470 LYS A 160 CG CD CE NZ 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 ALA A 119 -71.18 -60.86 REMARK 500 SER A 121 -87.38 -69.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 70 NE2 REMARK 620 2 HOH A 403 O 106.2 REMARK 620 3 HOH A 467 O 112.3 69.5 REMARK 620 4 HOH A 468 O 90.5 98.8 156.3 REMARK 620 5 HOH A 491 O 99.2 153.4 93.8 88.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 132 OD1 REMARK 620 2 ASP A 132 OD2 52.8 REMARK 620 3 ASP A 133 OD1 84.2 72.5 REMARK 620 4 ASP A 193 OD2 157.5 108.3 77.7 REMARK 620 5 ASN A 195 OD1 146.4 100.0 67.2 11.4 REMARK 620 6 ILE A 200 O 133.3 80.6 82.6 31.4 30.1 REMARK 620 7 HOH A 427 O 130.9 151.5 79.6 58.7 62.7 90.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 167 OD1 REMARK 620 2 ASN A 167 OD1 0.0 REMARK 620 3 HOH A 466 O 82.4 82.4 REMARK 620 4 HOH A 466 O 125.0 125.0 109.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 171 OE1 REMARK 620 2 GLU A 171 OE1 0.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2C2J RELATED DB: PDB REMARK 900 NATIVE DRDPS2 REMARK 900 RELATED ID: 2C6R RELATED DB: PDB REMARK 900 FE SOAKED DRDPS2 REMARK 900 RELATED ID: 6TB5 RELATED DB: PDB REMARK 900 CA, THEN FE SOAKED DRDPS2 REMARK 900 RELATED ID: SASDBF7 RELATED DB: SASBDB REMARK 900 DPS2, DNA BINDING PROTEIN UNDER STARVATION CONDITIONS (SEC-SAXS) DBREF 6TGT A 1 209 UNP Q9RZN1 DPS2_DEIRA 31 239 SEQRES 1 A 209 ASN GLY VAL PRO SER THR ASN VAL ASN THR PRO ALA PRO SEQRES 2 A 209 ASN THR GLY GLN SER THR ALA GLN ASN THR ASN THR ALA SEQRES 3 A 209 SER PRO LEU PRO TYR ASN ARG ALA THR THR LEU PRO ALA SEQRES 4 A 209 ALA GLY THR GLU ASP LEU LYS LYS SER VAL GLN ALA LEU SEQRES 5 A 209 GLN ASN THR LEU THR GLU LEU GLN ALA LEU GLN LEU GLN SEQRES 6 A 209 THR LYS GLN ALA HIS TRP ASN VAL SER GLY THR LEU TRP SEQRES 7 A 209 TYR THR LEU HIS GLU LEU LEU GLN ASP HIS TYR GLU GLY SEQRES 8 A 209 ILE SER LYS PHE ALA ASP ASP VAL ALA GLU ARG GLN LEU SEQRES 9 A 209 SER VAL GLY ALA SER SER ASP GLY ARG ALA ILE THR ILE SEQRES 10 A 209 VAL ALA ALA SER ARG LEU PRO GLU ILE PRO GLY GLY PHE SEQRES 11 A 209 LEU ASP ASP ALA GLN VAL ILE GLN PHE PHE THR TYR GLN SEQRES 12 A 209 TYR GLU THR VAL GLY GLN ARG ILE HIS GLN ARG VAL GLY SEQRES 13 A 209 ASP VAL GLU LYS VAL ASP PRO THR THR ALA ASN LEU LEU SEQRES 14 A 209 GLN GLU VAL GLU HIS ILE ILE GLU LYS TYR GLN TRP GLN SEQRES 15 A 209 MET ARG ALA PHE LEU GLN ASN THR PRO THR ASP PRO ASN SEQRES 16 A 209 THR GLY PHE ASP ILE ASN ASN GLY LYS PRO VAL PRO LEU SEQRES 17 A 209 ARG HET FE A 301 1 HET CA A 302 1 HET CA A 303 1 HET CA A 304 1 HETNAM FE FE (III) ION HETNAM CA CALCIUM ION FORMUL 2 FE FE 3+ FORMUL 3 CA 3(CA 2+) FORMUL 6 HOH *115(H2 O) HELIX 1 AA1 ASP A 44 ASN A 72 1 29 HELIX 2 AA2 LEU A 77 VAL A 106 1 30 HELIX 3 AA3 ARG A 113 ALA A 120 1 8 HELIX 4 AA4 ASP A 133 GLU A 159 1 27 HELIX 5 AA5 ASP A 162 ALA A 185 1 24 HELIX 6 AA6 PHE A 186 GLN A 188 5 3 HELIX 7 AA7 GLY A 197 ASN A 201 5 5 SHEET 1 AA1 2 VAL A 73 SER A 74 0 SHEET 2 AA1 2 LEU A 131 ASP A 132 1 O LEU A 131 N SER A 74 LINK NE2 HIS A 70 FE FE A 301 1555 1555 2.51 LINK OD1 ASP A 132 CA CA A 302 1555 1555 2.37 LINK OD2 ASP A 132 CA CA A 302 1555 1555 2.56 LINK OD1 ASP A 133 CA CA A 302 1555 1555 2.54 LINK OD1 ASN A 167 CA CA A 303 1555 1555 2.69 LINK OD1 ASN A 167 CA CA A 303 1555 9555 2.85 LINK OE1 GLU A 171 CA CA A 304 1555 1555 3.00 LINK OE1 GLU A 171 CA CA A 304 1555 9555 3.01 LINK OD2 ASP A 193 CA CA A 302 1555 11555 2.50 LINK OD1 ASN A 195 CA CA A 302 1555 11555 2.45 LINK O ILE A 200 CA CA A 302 1555 1555 2.48 LINK FE FE A 301 O AHOH A 403 1555 1555 1.95 LINK FE FE A 301 O AHOH A 467 1555 3555 2.53 LINK FE FE A 301 O HOH A 468 1555 1555 2.19 LINK FE FE A 301 O HOH A 491 1555 1555 2.13 LINK CA CA A 302 O HOH A 427 1555 1555 2.49 LINK CA CA A 303 O HOH A 466 1555 1555 2.69 LINK CA CA A 303 O HOH A 466 1555 5555 2.92 SITE 1 AC1 6 HIS A 70 TRP A 71 HOH A 403 HOH A 467 SITE 2 AC1 6 HOH A 468 HOH A 491 SITE 1 AC2 6 ASP A 132 ASP A 133 ASP A 193 ASN A 195 SITE 2 AC2 6 ILE A 200 HOH A 427 SITE 1 AC3 3 ASN A 167 GLN A 170 HOH A 466 SITE 1 AC4 2 ASN A 167 GLU A 171 CRYST1 88.342 88.342 88.342 90.00 90.00 90.00 P 2 3 12 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 0.011320 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011320 0.00000