HEADER DNA BINDING PROTEIN 17-JUL-23 8PV9 TITLE STRUCTURE OF DPS DETERMINED BY CRYOEM AT 100 KEV COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PROTECTION DURING STARVATION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 1.16.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DPS, PEXB, VTM, B0812, JW0797; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR G.MCMULLAN,K.NAYDENOVA,D.MIHAYLOV,M.J.PEET,H.WILSON,K.YAMASHITA, AUTHOR 2 J.L.DICKERSON,S.CHEN,G.CANNONE,Y.LEE,K.A.HUTCHINGS,O.GITTINS, AUTHOR 3 M.SOBHY,T.WELLS,M.M.EL-GOMATI,J.DALBY,M.MEFFERT,C.SCHULZE-BRIESE, AUTHOR 4 R.HENDERSON,C.J.RUSSO REVDAT 2 06-DEC-23 8PV9 1 JRNL REVDAT 1 29-NOV-23 8PV9 0 JRNL AUTH G.MCMULLAN,K.NAYDENOVA,D.MIHAYLOV,K.YAMASHITA,M.J.PEET, JRNL AUTH 2 H.WILSON,J.L.DICKERSON,S.CHEN,G.CANNONE,Y.LEE,K.A.HUTCHINGS, JRNL AUTH 3 O.GITTINS,M.A.SOBHY,T.WELLS,M.M.EL-GOMATI,J.DALBY,M.MEFFERT, JRNL AUTH 4 C.SCHULZE-BRIESE,R.HENDERSON,C.J.RUSSO JRNL TITL STRUCTURE DETERMINATION BY CRYOEM AT 100 KEV. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 05120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 38011573 JRNL DOI 10.1073/PNAS.2312905120 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERVALCAT REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6ZGL REMARK 3 REFINEMENT SPACE : RECIPROCAL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.700 REMARK 3 NUMBER OF PARTICLES : 48896 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8PV9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292131848. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : DNA PROTECTION DURING REMARK 245 STARVATION PROTEIN (DPS) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : JEOL 1400/HR + YPS FEG REMARK 245 DETECTOR TYPE : DECTRIS SINGLA (1K X 1K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 100 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 12-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 12-MERIC REMARK 350 SOFTWARE USED: PISA 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 -0.500000 -0.866025 0.000000 285.53195 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 76.50805 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 76.50805 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 285.53195 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.288675 0.816497 47.64788 REMARK 350 BIOMT2 4 -0.288675 0.833333 -0.471405 111.83975 REMARK 350 BIOMT3 4 -0.816497 -0.471405 -0.333333 316.33057 REMARK 350 BIOMT1 5 -0.500000 -0.288675 -0.816497 314.39212 REMARK 350 BIOMT2 5 0.288675 0.833333 -0.471405 42.16512 REMARK 350 BIOMT3 5 0.816497 -0.471405 -0.333333 119.26096 REMARK 350 BIOMT1 6 0.500000 -0.866025 0.000000 164.85195 REMARK 350 BIOMT2 6 -0.288675 -0.166667 0.942809 61.85245 REMARK 350 BIOMT3 6 -0.816497 -0.471405 -0.333333 316.33057 REMARK 350 BIOMT1 7 0.500000 -0.288675 -0.816497 193.71212 REMARK 350 BIOMT2 7 -0.866025 -0.166667 -0.471405 302.19438 REMARK 350 BIOMT3 7 0.000000 0.942809 -0.333333 47.12847 REMARK 350 BIOMT1 8 0.500000 0.288675 0.816497 -73.03212 REMARK 350 BIOMT2 8 0.866025 -0.166667 -0.471405 93.17048 REMARK 350 BIOMT3 8 0.000000 0.942809 -0.333333 47.12847 REMARK 350 BIOMT1 9 0.500000 0.866025 0.000000 -44.17195 REMARK 350 BIOMT2 9 0.288675 -0.166667 0.942809 -7.82218 REMARK 350 BIOMT3 9 0.816497 -0.471405 -0.333333 119.26095 REMARK 350 BIOMT1 10 0.000000 -0.577350 0.816497 91.81982 REMARK 350 BIOMT2 10 -0.577350 -0.666667 -0.471405 327.69706 REMARK 350 BIOMT3 10 0.816497 -0.471405 -0.333333 119.26096 REMARK 350 BIOMT1 11 0.000000 0.577350 -0.816497 149.54018 REMARK 350 BIOMT2 11 0.577350 -0.666667 -0.471405 188.34780 REMARK 350 BIOMT3 11 -0.816497 -0.471405 -0.333333 316.33057 REMARK 350 BIOMT1 12 -1.000000 0.000000 0.000000 241.36000 REMARK 350 BIOMT2 12 0.000000 0.333333 0.942809 -33.32486 REMARK 350 BIOMT3 12 0.000000 0.942809 -0.333333 47.12847 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 SER A 2 REMARK 465 THR A 3 REMARK 465 ALA A 4 REMARK 465 LYS A 5 REMARK 465 LEU A 6 REMARK 465 VAL A 7 REMARK 465 LYS A 8 REMARK 465 SER A 9 REMARK 465 LYS A 10 REMARK 465 ALA A 11 REMARK 465 THR A 12 REMARK 465 ASN A 13 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 HIS A 112 -40.45 -131.34 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 70 0.09 SIDE CHAIN REMARK 500 ARG A 124 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17958 RELATED DB: EMDB REMARK 900 STRUCTURE OF DPS DETERMINED BY CRYOEM AT 100 KEV DBREF 8PV9 A 2 167 UNP P0ABT2 DPS_ECOLI 2 167 SEQADV 8PV9 ALA A 27 UNP P0ABT2 LYS 27 CONFLICT SEQRES 1 A 166 SER THR ALA LYS LEU VAL LYS SER LYS ALA THR ASN LEU SEQRES 2 A 166 LEU TYR THR ARG ASN ASP VAL SER ASP SER GLU LYS ALA SEQRES 3 A 166 ALA THR VAL GLU LEU LEU ASN ARG GLN VAL ILE GLN PHE SEQRES 4 A 166 ILE ASP LEU SER LEU ILE THR LYS GLN ALA HIS TRP ASN SEQRES 5 A 166 MET ARG GLY ALA ASN PHE ILE ALA VAL HIS GLU MET LEU SEQRES 6 A 166 ASP GLY PHE ARG THR ALA LEU ILE ASP HIS LEU ASP THR SEQRES 7 A 166 MET ALA GLU ARG ALA VAL GLN LEU GLY GLY VAL ALA LEU SEQRES 8 A 166 GLY THR THR GLN VAL ILE ASN SER LYS THR PRO LEU LYS SEQRES 9 A 166 SER TYR PRO LEU ASP ILE HIS ASN VAL GLN ASP HIS LEU SEQRES 10 A 166 LYS GLU LEU ALA ASP ARG TYR ALA ILE VAL ALA ASN ASP SEQRES 11 A 166 VAL ARG LYS ALA ILE GLY GLU ALA LYS ASP ASP ASP THR SEQRES 12 A 166 ALA ASP ILE LEU THR ALA ALA SER ARG ASP LEU ASP LYS SEQRES 13 A 166 PHE LEU TRP PHE ILE GLU SER ASN ILE GLU HELIX 1 AA1 SER A 22 MET A 54 1 33 HELIX 2 AA2 ASN A 58 LEU A 87 1 30 HELIX 3 AA3 THR A 94 THR A 102 1 9 HELIX 4 AA4 ASN A 113 ALA A 139 1 27 HELIX 5 AA5 ASP A 141 ASN A 165 1 25 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.500000 -0.866025 0.000000 285.53195 MTRIX2 2 0.866025 -0.500000 0.000000 76.50805 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 -0.500000 0.866025 0.000000 76.50805 MTRIX2 3 -0.866025 -0.500000 0.000000 285.53195 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 MTRIX1 4 -0.500000 0.288675 0.816497 47.64788 MTRIX2 4 -0.288675 0.833333 -0.471405 111.83975 MTRIX3 4 -0.816497 -0.471405 -0.333333 316.33057 MTRIX1 5 -0.500000 -0.288675 -0.816497 314.39212 MTRIX2 5 0.288675 0.833333 -0.471405 42.16512 MTRIX3 5 0.816497 -0.471405 -0.333333 119.26096 MTRIX1 6 0.500000 -0.866025 0.000000 164.85195 MTRIX2 6 -0.288675 -0.166667 0.942809 61.85245 MTRIX3 6 -0.816497 -0.471405 -0.333333 316.33057 MTRIX1 7 0.500000 -0.288675 -0.816497 193.71212 MTRIX2 7 -0.866025 -0.166667 -0.471405 302.19438 MTRIX3 7 0.000000 0.942809 -0.333333 47.12847 MTRIX1 8 0.500000 0.288675 0.816497 -73.03212 MTRIX2 8 0.866025 -0.166667 -0.471405 93.17048 MTRIX3 8 0.000000 0.942809 -0.333333 47.12847 MTRIX1 9 0.500000 0.866025 0.000000 -44.17195 MTRIX2 9 0.288675 -0.166667 0.942809 -7.82218 MTRIX3 9 0.816497 -0.471405 -0.333333 119.26095 MTRIX1 10 0.000000 -0.577350 0.816497 91.81982 MTRIX2 10 -0.577350 -0.666667 -0.471405 327.69706 MTRIX3 10 0.816497 -0.471405 -0.333333 119.26096 MTRIX1 11 0.000000 0.577350 -0.816497 149.54018 MTRIX2 11 0.577350 -0.666667 -0.471405 188.34780 MTRIX3 11 -0.816497 -0.471405 -0.333333 316.33057 MTRIX1 12 -1.000000 0.000000 0.000000 241.36000 MTRIX2 12 0.000000 0.333333 0.942809 -33.32486 MTRIX3 12 0.000000 0.942809 -0.333333 47.12847