HEADER STRUCTURAL PROTEIN 07-NOV-23 8X1I TITLE PARM PRESENT OF GENOME OF DESUFITOBACTERIUM HAFNIENSE - DH-CPARM1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARM PRESENT OF GENOME OF DESUFITOBACTERIUM HAFNIENSE - DH- COMPND 3 CPARM1; COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: GENOME ENCODE PARM1 FROM DESULFITOBACTERIUM SPECIES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFITOBACTERIUM HAFNIENSE Y51; SOURCE 3 ORGANISM_TAXID: 138119; SOURCE 4 GENE: DSY2109; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PARM, GENOME, SEGREGATION, PLASMID, STRUCTURAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.ALI,R.C.ROBINSON,A.NARITA REVDAT 1 13-NOV-24 8X1I 0 JRNL AUTH S.ALI,R.C.ROBINSON,A.NARITA JRNL TITL BACTERIAL GENOME ENCODED PARMS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, UCSF CHIMERA, ISOLDE, RELION, REMARK 3 RELION REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : INITIAL FITTING WAS PERFORMED USING CHIMERA REMARK 3 AND MDFF PERFORMED BY ISOLDE AND FINAL REAL SPACE REFINE BY REMARK 3 PHENIX REAL SPACE REFINEMENT. 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) : 4.000 REMARK 3 NUMBER OF PARTICLES : 2100 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 8X1I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042233. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : DH-CPARM1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 10.00 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 : PARM PRESENT OF GENOME OF REMARK 245 DESUFITOBACTERIUM HAFNIENSE - DH-CPARM1 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 300 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 ASP B 5 46.08 -80.64 REMARK 500 ALA B 31 41.23 -78.61 REMARK 500 ARG B 39 18.83 58.45 REMARK 500 SER B 61 38.62 -85.91 REMARK 500 LEU B 86 -60.53 -122.22 REMARK 500 ASN B 87 56.19 -117.04 REMARK 500 TRP B 95 55.82 -145.32 REMARK 500 LEU B 138 -31.14 -133.38 REMARK 500 LEU B 146 58.32 -92.71 REMARK 500 ASN B 271 40.61 -144.33 REMARK 500 THR B 362 -62.73 -124.18 REMARK 500 LYS B 363 93.24 -162.55 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 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 206 OD2 REMARK 620 2 ADP B 401 O1B 140.5 REMARK 620 3 ADP B 401 O2B 142.0 71.8 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37996 RELATED DB: EMDB DBREF 8X1I B 1 369 UNP Q24VP4 Q24VP4_DESHY 1 369 SEQRES 1 B 369 MET PHE GLU ASN ASP ILE LEU VAL ALA GLY GLY ASP PRO SEQRES 2 B 369 GLY PHE GLY ALA ILE LYS LEU ASP ALA GLY ASP THR LYS SEQRES 3 B 369 VAL LEU PHE PRO ALA VAL ILE CYS LYS GLY ASN GLU ARG SEQRES 4 B 369 ILE PHE SER ALA LEU GLY ASN GLY ASN VAL SER ARG GLY SEQRES 5 B 369 THR ASP GLU GLU MET GLN THR GLY SER LEU ASP VAL ILE SEQRES 6 B 369 VAL THR ASN HIS SER THR GLY VAL SER ARG HIS TYR PHE SEQRES 7 B 369 MET GLY SER LEU ALA GLU SER LEU ASN PRO ASN GLU ALA SEQRES 8 B 369 HIS TYR CYS TRP ASP GLU ASP LYS SER THR ASP GLU GLU SEQRES 9 B 369 ALA THR ALA LEU LEU VAL VAL ALA LEU ALA VAL ALA GLN SEQRES 10 B 369 LYS GLU PRO LYS ALA ASN ILE TYR LEU GLY THR GLY VAL SEQRES 11 B 369 PRO VAL LYS TYR TYR ALA ALA LEU LYS ASP LYS TYR GLU SEQRES 12 B 369 ALA GLU LEU LYS GLY THR TRP SER VAL ALA PHE ARG SER SEQRES 13 B 369 GLY PRO PHE LYS GLY GLN THR ARG GLN LEU THR ILE ILE SEQRES 14 B 369 ARG SER ARG VAL LEU PRO GLN SER TYR GLY VAL PHE ILE SEQRES 15 B 369 LYS GLU THR LEU ASN GLU TYR GLY ILE PRO ILE SER PRO SEQRES 16 B 369 LYS LEU PHE ASN GLY TYR VAL VAL VAL ILE ASP PRO GLY SEQRES 17 B 369 PHE ARG THR THR ASP VAL ALA THR PHE TYR ASP GLY VAL SEQRES 18 B 369 MET LEU ASP PRO PRO ASN SER PHE SER ILE GLU LYS GLY SEQRES 19 B 369 LEU LYS TRP ALA TYR THR GLY VAL ALA GLU GLN LEU LYS SEQRES 20 B 369 GLU MET THR ILE ASN HIS ALA ASN PRO ILE GLU THR ASP SEQRES 21 B 369 ASP LYS GLU LEU ASP LYS VAL PHE ARG VAL ASN GLU GLY SEQRES 22 B 369 MET TYR PRO TRP ASN ASN GLY ALA ILE ASN LEU ASN PRO SEQRES 23 B 369 VAL MET GLN ASP MET LEU GLY GLN LEU GLY THR ASP ILE SEQRES 24 B 369 SER ARG GLU VAL LYS LYS SER LEU LYS PRO MET LEU GLY SEQRES 25 B 369 LYS ILE HIS THR VAL LEU VAL ALA GLY LYS VAL GLY GLU SEQRES 26 B 369 MET ILE PHE GLU HIS LEU GLN PHE GLU ASN LYS VAL LEU SEQRES 27 B 369 ILE GLU ASN PRO GLN PHE GLY ASN ALA THR GLY PHE ARG SEQRES 28 B 369 ILE MET ALA ALA ASN LEU VAL ASN ASN ILE THR LYS LYS SEQRES 29 B 369 ALA ASN ALA ALA PRO HET ADP B 401 39 HET MG B 402 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG MG 2+ HELIX 1 AA1 LEU B 44 ASN B 48 5 5 HELIX 2 AA2 GLU B 55 THR B 59 5 5 HELIX 3 AA3 GLY B 80 SER B 85 1 6 HELIX 4 AA4 ASP B 102 GLN B 117 1 16 HELIX 5 AA5 PRO B 131 TYR B 135 5 5 HELIX 6 AA6 LEU B 138 LEU B 146 1 9 HELIX 7 AA7 SER B 156 LYS B 160 5 5 HELIX 8 AA8 SER B 177 LEU B 186 1 10 HELIX 9 AA9 SER B 194 PHE B 198 5 5 HELIX 10 AB1 ASP B 224 PRO B 226 5 3 HELIX 11 AB2 GLY B 234 MET B 249 1 16 HELIX 12 AB3 ASP B 260 GLU B 272 1 13 HELIX 13 AB4 LEU B 284 LYS B 308 1 25 HELIX 14 AB5 PRO B 309 GLY B 312 5 4 HELIX 15 AB6 ALA B 320 PHE B 328 1 9 HELIX 16 AB7 GLU B 329 LEU B 331 5 3 HELIX 17 AB8 ASN B 341 GLN B 343 5 3 HELIX 18 AB9 PHE B 344 LEU B 357 1 14 HELIX 19 AC1 ASN B 359 LYS B 364 1 6 SHEET 1 AA110 LYS B 26 PRO B 30 0 SHEET 2 AA110 ALA B 17 ASP B 21 -1 N ILE B 18 O PHE B 29 SHEET 3 AA110 LEU B 7 GLY B 11 -1 N GLY B 10 O ASP B 21 SHEET 4 AA110 LYS B 121 THR B 128 1 O TYR B 125 N LEU B 7 SHEET 5 AA110 GLN B 165 VAL B 173 1 O ILE B 169 N ILE B 124 SHEET 6 AA110 GLY B 148 PHE B 154 -1 N TRP B 150 O LEU B 166 SHEET 7 AA110 LEU B 62 THR B 67 -1 N THR B 67 O SER B 151 SHEET 8 AA110 SER B 74 MET B 79 -1 O ARG B 75 N VAL B 66 SHEET 9 AA110 VAL B 32 CYS B 34 -1 N CYS B 34 O PHE B 78 SHEET 10 AA110 HIS B 92 TYR B 93 -1 O HIS B 92 N ILE B 33 SHEET 1 AA2 3 VAL B 221 MET B 222 0 SHEET 2 AA2 3 THR B 212 TYR B 218 -1 N TYR B 218 O VAL B 221 SHEET 3 AA2 3 SER B 228 ILE B 231 -1 O ILE B 231 N THR B 212 SHEET 1 AA3 5 VAL B 221 MET B 222 0 SHEET 2 AA3 5 THR B 212 TYR B 218 -1 N TYR B 218 O VAL B 221 SHEET 3 AA3 5 TYR B 201 PRO B 207 -1 N VAL B 202 O PHE B 217 SHEET 4 AA3 5 ILE B 314 VAL B 319 1 O LEU B 318 N VAL B 203 SHEET 5 AA3 5 LYS B 336 LEU B 338 1 O VAL B 337 N VAL B 319 SHEET 1 AA4 2 MET B 274 TRP B 277 0 SHEET 2 AA4 2 GLY B 280 ASN B 283 -1 O ILE B 282 N TYR B 275 LINK OD2 ASP B 206 MG MG B 402 1555 1555 1.89 LINK O1B ADP B 401 MG MG B 402 1555 1555 1.91 LINK O2B ADP B 401 MG MG B 402 1555 1555 1.89 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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