HEADER CYTOSOLIC PROTEIN 04-JUL-23 8POC TITLE CRYO-EM STRUCTURE OF DICKEYA DADANTII BCSD COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULOSE SYNTHASE OPERON PROTEIN D; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICKEYA DADANTII 3937; SOURCE 3 ORGANISM_TAXID: 198628; SOURCE 4 GENE: BCSD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CELLULOSE SECRETION, BACTERIAL BIOFILMS, CYTOSKELETON, CYTOSOLIC KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.NOTOPOULOU,P.V.KRASTEVA REVDAT 3 24-JAN-24 8POC 1 JRNL REVDAT 2 03-JAN-24 8POC 1 JRNL REVDAT 1 20-DEC-23 8POC 0 JRNL AUTH T.G.SANA,A.NOTOPOULOU,L.PUYGRENIER,M.DECOSSAS,S.MOREAU, JRNL AUTH 2 A.CARLIER,P.V.KRASTEVA JRNL TITL STRUCTURES AND ROLES OF BCSD AND PARTNER SCAFFOLD PROTEINS JRNL TITL 2 IN PROTEOBACTERIAL CELLULOSE SECRETION. JRNL REF CURR.BIOL. V. 34 106 2024 JRNL REFN ISSN 0960-9822 JRNL PMID 38141614 JRNL DOI 10.1016/J.CUB.2023.11.057 REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, GCTF, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX, COOT REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : REITERATIVE REFINEMENT IN PHENIX, COOT AND REMARK 3 NAMDINATOR 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 : 295199 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 8POC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292131648. 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 : TETRAMERIC BCSD OF DICKEYA REMARK 245 DADANTII REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2600.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5290.00 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) : 200 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 HIS A 155 REMARK 465 MET B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 HIS B 155 REMARK 465 MET C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 HIS C 155 REMARK 465 MET D -2 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 HIS D 155 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 D 90 11.59 -140.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17735 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-17788 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF DICKEYA DADANTII BCSD DBREF 8POC A 1 155 UNP E0SES7 E0SES7_DICD3 1 155 DBREF 8POC B 1 155 UNP E0SES7 E0SES7_DICD3 1 155 DBREF 8POC C 1 155 UNP E0SES7 E0SES7_DICD3 1 155 DBREF 8POC D 1 155 UNP E0SES7 E0SES7_DICD3 1 155 SEQADV 8POC MET A -2 UNP E0SES7 INITIATING METHIONINE SEQADV 8POC GLY A -1 UNP E0SES7 EXPRESSION TAG SEQADV 8POC SER A 0 UNP E0SES7 EXPRESSION TAG SEQADV 8POC MET B -2 UNP E0SES7 INITIATING METHIONINE SEQADV 8POC GLY B -1 UNP E0SES7 EXPRESSION TAG SEQADV 8POC SER B 0 UNP E0SES7 EXPRESSION TAG SEQADV 8POC MET C -2 UNP E0SES7 INITIATING METHIONINE SEQADV 8POC GLY C -1 UNP E0SES7 EXPRESSION TAG SEQADV 8POC SER C 0 UNP E0SES7 EXPRESSION TAG SEQADV 8POC MET D -2 UNP E0SES7 INITIATING METHIONINE SEQADV 8POC GLY D -1 UNP E0SES7 EXPRESSION TAG SEQADV 8POC SER D 0 UNP E0SES7 EXPRESSION TAG SEQRES 1 A 158 MET GLY SER MET SER ASP LEU GLN GLN HIS ALA LEU ASN SEQRES 2 A 158 TYR TYR ARG GLN GLN GLN LEU PRO SER GLY TRP ALA ASP SEQRES 3 A 158 LEU PHE GLY VAL ILE VAL ASN GLY MET MET ASP ASN ALA SEQRES 4 A 158 GLY GLU ARG GLU GLY LEU ALA PHE LEU ARG HIS ILE GLY SEQRES 5 A 158 GLY GLN LEU ALA GLU ARG TYR PRO LEU PRO ALA ALA VAL SEQRES 6 A 158 THR VAL VAL ASP LEU GLU ARG GLU ILE ASN ARG VAL LEU SEQRES 7 A 158 SER LEU PHE HIS TRP GLY CYS VAL ASP LEU ARG PRO TYR SEQRES 8 A 158 GLU ASN ARG LEU GLU ILE TYR HIS LEU ALA LEU PRO ALA SEQRES 9 A 158 SER VAL ASN SER SER GLY SER VAL ARG TRP ARG MET ALA SEQRES 10 A 158 MET ALA ALA VAL LEU GLN GLY LEU TYR SER ARG TRP LEU SEQRES 11 A 158 ARG GLU GLN GLY GLY VAL GLU SER VAL PRO LEU SER CYS SEQRES 12 A 158 GLU GLU THR ASP SER GLU SER THR LEU LEU PHE ARG TYR SEQRES 13 A 158 GLN HIS SEQRES 1 B 158 MET GLY SER MET SER ASP LEU GLN GLN HIS ALA LEU ASN SEQRES 2 B 158 TYR TYR ARG GLN GLN GLN LEU PRO SER GLY TRP ALA ASP SEQRES 3 B 158 LEU PHE GLY VAL ILE VAL ASN GLY MET MET ASP ASN ALA SEQRES 4 B 158 GLY GLU ARG GLU GLY LEU ALA PHE LEU ARG HIS ILE GLY SEQRES 5 B 158 GLY GLN LEU ALA GLU ARG TYR PRO LEU PRO ALA ALA VAL SEQRES 6 B 158 THR VAL VAL ASP LEU GLU ARG GLU ILE ASN ARG VAL LEU SEQRES 7 B 158 SER LEU PHE HIS TRP GLY CYS VAL ASP LEU ARG PRO TYR SEQRES 8 B 158 GLU ASN ARG LEU GLU ILE TYR HIS LEU ALA LEU PRO ALA SEQRES 9 B 158 SER VAL ASN SER SER GLY SER VAL ARG TRP ARG MET ALA SEQRES 10 B 158 MET ALA ALA VAL LEU GLN GLY LEU TYR SER ARG TRP LEU SEQRES 11 B 158 ARG GLU GLN GLY GLY VAL GLU SER VAL PRO LEU SER CYS SEQRES 12 B 158 GLU GLU THR ASP SER GLU SER THR LEU LEU PHE ARG TYR SEQRES 13 B 158 GLN HIS SEQRES 1 C 158 MET GLY SER MET SER ASP LEU GLN GLN HIS ALA LEU ASN SEQRES 2 C 158 TYR TYR ARG GLN GLN GLN LEU PRO SER GLY TRP ALA ASP SEQRES 3 C 158 LEU PHE GLY VAL ILE VAL ASN GLY MET MET ASP ASN ALA SEQRES 4 C 158 GLY GLU ARG GLU GLY LEU ALA PHE LEU ARG HIS ILE GLY SEQRES 5 C 158 GLY GLN LEU ALA GLU ARG TYR PRO LEU PRO ALA ALA VAL SEQRES 6 C 158 THR VAL VAL ASP LEU GLU ARG GLU ILE ASN ARG VAL LEU SEQRES 7 C 158 SER LEU PHE HIS TRP GLY CYS VAL ASP LEU ARG PRO TYR SEQRES 8 C 158 GLU ASN ARG LEU GLU ILE TYR HIS LEU ALA LEU PRO ALA SEQRES 9 C 158 SER VAL ASN SER SER GLY SER VAL ARG TRP ARG MET ALA SEQRES 10 C 158 MET ALA ALA VAL LEU GLN GLY LEU TYR SER ARG TRP LEU SEQRES 11 C 158 ARG GLU GLN GLY GLY VAL GLU SER VAL PRO LEU SER CYS SEQRES 12 C 158 GLU GLU THR ASP SER GLU SER THR LEU LEU PHE ARG TYR SEQRES 13 C 158 GLN HIS SEQRES 1 D 158 MET GLY SER MET SER ASP LEU GLN GLN HIS ALA LEU ASN SEQRES 2 D 158 TYR TYR ARG GLN GLN GLN LEU PRO SER GLY TRP ALA ASP SEQRES 3 D 158 LEU PHE GLY VAL ILE VAL ASN GLY MET MET ASP ASN ALA SEQRES 4 D 158 GLY GLU ARG GLU GLY LEU ALA PHE LEU ARG HIS ILE GLY SEQRES 5 D 158 GLY GLN LEU ALA GLU ARG TYR PRO LEU PRO ALA ALA VAL SEQRES 6 D 158 THR VAL VAL ASP LEU GLU ARG GLU ILE ASN ARG VAL LEU SEQRES 7 D 158 SER LEU PHE HIS TRP GLY CYS VAL ASP LEU ARG PRO TYR SEQRES 8 D 158 GLU ASN ARG LEU GLU ILE TYR HIS LEU ALA LEU PRO ALA SEQRES 9 D 158 SER VAL ASN SER SER GLY SER VAL ARG TRP ARG MET ALA SEQRES 10 D 158 MET ALA ALA VAL LEU GLN GLY LEU TYR SER ARG TRP LEU SEQRES 11 D 158 ARG GLU GLN GLY GLY VAL GLU SER VAL PRO LEU SER CYS SEQRES 12 D 158 GLU GLU THR ASP SER GLU SER THR LEU LEU PHE ARG TYR SEQRES 13 D 158 GLN HIS HELIX 1 AA1 SER A 2 GLN A 15 1 14 HELIX 2 AA2 GLY A 20 GLY A 37 1 18 HELIX 3 AA3 GLU A 38 TYR A 56 1 19 HELIX 4 AA4 THR A 63 HIS A 79 1 17 HELIX 5 AA5 GLY A 107 GLY A 131 1 25 HELIX 6 AA6 SER B 2 GLN B 15 1 14 HELIX 7 AA7 GLY B 20 GLY B 37 1 18 HELIX 8 AA8 GLU B 38 TYR B 56 1 19 HELIX 9 AA9 THR B 63 HIS B 79 1 17 HELIX 10 AB1 GLY B 107 GLN B 130 1 24 HELIX 11 AB2 SER C 2 GLN C 15 1 14 HELIX 12 AB3 GLY C 20 GLY C 37 1 18 HELIX 13 AB4 GLU C 38 TYR C 56 1 19 HELIX 14 AB5 THR C 63 HIS C 79 1 17 HELIX 15 AB6 GLY C 107 GLN C 130 1 24 HELIX 16 AB7 SER D 2 GLN D 15 1 14 HELIX 17 AB8 GLY D 20 GLY D 37 1 18 HELIX 18 AB9 GLU D 38 TYR D 56 1 19 HELIX 19 AC1 THR D 63 HIS D 79 1 17 HELIX 20 AC2 GLY D 107 GLY D 131 1 25 SHEET 1 AA1 4 CYS A 82 PRO A 87 0 SHEET 2 AA1 4 LEU A 92 LEU A 97 -1 O GLU A 93 N ARG A 86 SHEET 3 AA1 4 LEU A 149 TYR A 153 -1 O LEU A 149 N HIS A 96 SHEET 4 AA1 4 SER A 139 GLU A 142 -1 N GLU A 141 O LEU A 150 SHEET 1 AA2 4 CYS B 82 PRO B 87 0 SHEET 2 AA2 4 LEU B 92 LEU B 97 -1 O GLU B 93 N ARG B 86 SHEET 3 AA2 4 THR B 148 TYR B 153 -1 O PHE B 151 N ILE B 94 SHEET 4 AA2 4 LEU B 138 GLU B 142 -1 N GLU B 141 O LEU B 150 SHEET 1 AA3 4 CYS C 82 PRO C 87 0 SHEET 2 AA3 4 LEU C 92 LEU C 97 -1 O GLU C 93 N ARG C 86 SHEET 3 AA3 4 LEU C 149 TYR C 153 -1 O LEU C 149 N HIS C 96 SHEET 4 AA3 4 SER C 139 GLU C 142 -1 N GLU C 141 O LEU C 150 SHEET 1 AA4 4 CYS D 82 PRO D 87 0 SHEET 2 AA4 4 LEU D 92 LEU D 97 -1 O GLU D 93 N ARG D 86 SHEET 3 AA4 4 LEU D 149 TYR D 153 -1 O LEU D 149 N HIS D 96 SHEET 4 AA4 4 SER D 139 GLU D 142 -1 N GLU D 141 O LEU D 150 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