HEADER STRUCTURAL PROTEIN 26-JUN-23 8PKD TITLE CRYO-EM STRUCTURE OF ORRELLA DIOSCOREAE 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: ORRELLA DIOSCOREAE; SOURCE 3 ORGANISM_TAXID: 1851544; SOURCE 4 GENE: ODI_03820; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BACTERIAL CYTOSKELETON, BACTERIAL CELLULOSE, BACTERIAL SECRETION, KEYWDS 2 BACTERIAL BIOFILMS, STRUCTURAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR L.PUYGRENIER,M.DECOSSAS,P.V.KRASTEVA REVDAT 3 24-JAN-24 8PKD 1 JRNL REVDAT 2 03-JAN-24 8PKD 1 JRNL REVDAT 1 20-DEC-23 8PKD 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. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, GCTF, COOT, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX 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 : ITERATIVE MODEL BUILDING AND REFINEMENT IN REMARK 3 COOT, NAMDINATOR AND PHENIX. 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) : 2.330 REMARK 3 NUMBER OF PARTICLES : 203260 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: ALL REFINEMENTS (HETEROREFINEMENT AND NON-UNIFORM REMARK 3 REFINEMENT PERFORMED IN CRYOSPARC) REMARK 4 REMARK 4 8PKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131483. 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 : ORRELLA DIOSCOREAE BCSD 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 : 19118 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 5160.00 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 MET B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 MET C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 MET C 1 REMARK 465 MET D -2 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 MET D 1 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 A 86 -97.23 54.11 REMARK 500 ASP B 86 -97.74 53.35 REMARK 500 ASP C 86 -97.82 53.82 REMARK 500 ASP D 86 -97.33 53.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17735 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ORRELLA DIOSCOREAE BCSD DBREF1 8PKD A 1 151 UNP A0A1C3K6W2_9BURK DBREF2 8PKD A A0A1C3K6W2 1 151 DBREF1 8PKD B 1 151 UNP A0A1C3K6W2_9BURK DBREF2 8PKD B A0A1C3K6W2 1 151 DBREF1 8PKD C 1 151 UNP A0A1C3K6W2_9BURK DBREF2 8PKD C A0A1C3K6W2 1 151 DBREF1 8PKD D 1 151 UNP A0A1C3K6W2_9BURK DBREF2 8PKD D A0A1C3K6W2 1 151 SEQADV 8PKD MET A -2 UNP A0A1C3K6W INITIATING METHIONINE SEQADV 8PKD GLY A -1 UNP A0A1C3K6W EXPRESSION TAG SEQADV 8PKD SER A 0 UNP A0A1C3K6W EXPRESSION TAG SEQADV 8PKD MET B -2 UNP A0A1C3K6W INITIATING METHIONINE SEQADV 8PKD GLY B -1 UNP A0A1C3K6W EXPRESSION TAG SEQADV 8PKD SER B 0 UNP A0A1C3K6W EXPRESSION TAG SEQADV 8PKD MET C -2 UNP A0A1C3K6W INITIATING METHIONINE SEQADV 8PKD GLY C -1 UNP A0A1C3K6W EXPRESSION TAG SEQADV 8PKD SER C 0 UNP A0A1C3K6W EXPRESSION TAG SEQADV 8PKD MET D -2 UNP A0A1C3K6W INITIATING METHIONINE SEQADV 8PKD GLY D -1 UNP A0A1C3K6W EXPRESSION TAG SEQADV 8PKD SER D 0 UNP A0A1C3K6W EXPRESSION TAG SEQRES 1 A 154 MET GLY SER MET GLU ASN PRO LEU PHE ASP TYR TYR ARG SEQRES 2 A 154 ASN ARG GLN ALA PRO LEU GLN TRP ARG GLY ALA LEU GLY SEQRES 3 A 154 ALA LEU ALA GLN SER LEU THR ASN HIS PHE SER PRO GLU SEQRES 4 A 154 GLN LEU ARG THR LEU LEU ARG GLU ALA GLY GLN HIS PHE SEQRES 5 A 154 ALA SER GLN HIS PRO VAL GLN ALA ALA GLU THR VAL GLN SEQRES 6 A 154 SER MET GLN ASP ALA MET ASN GLY VAL TRP THR THR GLN SEQRES 7 A 154 ASP TRP GLY TRP VAL ASP ILE HIS ASP LEU ASP SER PHE SEQRES 8 A 154 LEU THR LEU THR HIS TYR ALA ALA PRO LEU GLU SER ALA SEQRES 9 A 154 PHE GLY ALA GLN ASN LEU ALA TRP SER ALA ALA PHE LEU SEQRES 10 A 154 GLU GLY VAL TYR GLU GLN TRP PHE ARG GLN LEU GLY ALA SEQRES 11 A 154 SER ASP ALA LEU HIS VAL ARG GLN SER GLU GLU SER ASP SEQRES 12 A 154 VAL ARG LYS ALA ILE VAL LEU ARG LEU GLY ARG SEQRES 1 B 154 MET GLY SER MET GLU ASN PRO LEU PHE ASP TYR TYR ARG SEQRES 2 B 154 ASN ARG GLN ALA PRO LEU GLN TRP ARG GLY ALA LEU GLY SEQRES 3 B 154 ALA LEU ALA GLN SER LEU THR ASN HIS PHE SER PRO GLU SEQRES 4 B 154 GLN LEU ARG THR LEU LEU ARG GLU ALA GLY GLN HIS PHE SEQRES 5 B 154 ALA SER GLN HIS PRO VAL GLN ALA ALA GLU THR VAL GLN SEQRES 6 B 154 SER MET GLN ASP ALA MET ASN GLY VAL TRP THR THR GLN SEQRES 7 B 154 ASP TRP GLY TRP VAL ASP ILE HIS ASP LEU ASP SER PHE SEQRES 8 B 154 LEU THR LEU THR HIS TYR ALA ALA PRO LEU GLU SER ALA SEQRES 9 B 154 PHE GLY ALA GLN ASN LEU ALA TRP SER ALA ALA PHE LEU SEQRES 10 B 154 GLU GLY VAL TYR GLU GLN TRP PHE ARG GLN LEU GLY ALA SEQRES 11 B 154 SER ASP ALA LEU HIS VAL ARG GLN SER GLU GLU SER ASP SEQRES 12 B 154 VAL ARG LYS ALA ILE VAL LEU ARG LEU GLY ARG SEQRES 1 C 154 MET GLY SER MET GLU ASN PRO LEU PHE ASP TYR TYR ARG SEQRES 2 C 154 ASN ARG GLN ALA PRO LEU GLN TRP ARG GLY ALA LEU GLY SEQRES 3 C 154 ALA LEU ALA GLN SER LEU THR ASN HIS PHE SER PRO GLU SEQRES 4 C 154 GLN LEU ARG THR LEU LEU ARG GLU ALA GLY GLN HIS PHE SEQRES 5 C 154 ALA SER GLN HIS PRO VAL GLN ALA ALA GLU THR VAL GLN SEQRES 6 C 154 SER MET GLN ASP ALA MET ASN GLY VAL TRP THR THR GLN SEQRES 7 C 154 ASP TRP GLY TRP VAL ASP ILE HIS ASP LEU ASP SER PHE SEQRES 8 C 154 LEU THR LEU THR HIS TYR ALA ALA PRO LEU GLU SER ALA SEQRES 9 C 154 PHE GLY ALA GLN ASN LEU ALA TRP SER ALA ALA PHE LEU SEQRES 10 C 154 GLU GLY VAL TYR GLU GLN TRP PHE ARG GLN LEU GLY ALA SEQRES 11 C 154 SER ASP ALA LEU HIS VAL ARG GLN SER GLU GLU SER ASP SEQRES 12 C 154 VAL ARG LYS ALA ILE VAL LEU ARG LEU GLY ARG SEQRES 1 D 154 MET GLY SER MET GLU ASN PRO LEU PHE ASP TYR TYR ARG SEQRES 2 D 154 ASN ARG GLN ALA PRO LEU GLN TRP ARG GLY ALA LEU GLY SEQRES 3 D 154 ALA LEU ALA GLN SER LEU THR ASN HIS PHE SER PRO GLU SEQRES 4 D 154 GLN LEU ARG THR LEU LEU ARG GLU ALA GLY GLN HIS PHE SEQRES 5 D 154 ALA SER GLN HIS PRO VAL GLN ALA ALA GLU THR VAL GLN SEQRES 6 D 154 SER MET GLN ASP ALA MET ASN GLY VAL TRP THR THR GLN SEQRES 7 D 154 ASP TRP GLY TRP VAL ASP ILE HIS ASP LEU ASP SER PHE SEQRES 8 D 154 LEU THR LEU THR HIS TYR ALA ALA PRO LEU GLU SER ALA SEQRES 9 D 154 PHE GLY ALA GLN ASN LEU ALA TRP SER ALA ALA PHE LEU SEQRES 10 D 154 GLU GLY VAL TYR GLU GLN TRP PHE ARG GLN LEU GLY ALA SEQRES 11 D 154 SER ASP ALA LEU HIS VAL ARG GLN SER GLU GLU SER ASP SEQRES 12 D 154 VAL ARG LYS ALA ILE VAL LEU ARG LEU GLY ARG FORMUL 5 HOH *16(H2 O) HELIX 1 AA1 GLU A 2 ARG A 12 1 11 HELIX 2 AA2 TRP A 18 PHE A 33 1 16 HELIX 3 AA3 SER A 34 HIS A 53 1 20 HELIX 4 AA4 THR A 60 THR A 74 1 15 HELIX 5 AA5 PRO A 97 GLY A 103 1 7 HELIX 6 AA6 ASN A 106 ALA A 111 1 6 HELIX 7 AA7 ALA A 111 LEU A 125 1 15 HELIX 8 AA8 ASN B 3 ARG B 12 1 10 HELIX 9 AA9 TRP B 18 PHE B 33 1 16 HELIX 10 AB1 SER B 34 HIS B 53 1 20 HELIX 11 AB2 THR B 60 THR B 74 1 15 HELIX 12 AB3 PRO B 97 GLY B 103 1 7 HELIX 13 AB4 ASN B 106 ALA B 111 1 6 HELIX 14 AB5 ALA B 111 LEU B 125 1 15 HELIX 15 AB6 ASN C 3 ARG C 12 1 10 HELIX 16 AB7 TRP C 18 PHE C 33 1 16 HELIX 17 AB8 SER C 34 HIS C 53 1 20 HELIX 18 AB9 THR C 60 THR C 74 1 15 HELIX 19 AC1 PRO C 97 GLY C 103 1 7 HELIX 20 AC2 ASN C 106 ALA C 111 1 6 HELIX 21 AC3 ALA C 111 LEU C 125 1 15 HELIX 22 AC4 ASN D 3 ARG D 12 1 10 HELIX 23 AC5 TRP D 18 PHE D 33 1 16 HELIX 24 AC6 SER D 34 HIS D 53 1 20 HELIX 25 AC7 THR D 60 THR D 74 1 15 HELIX 26 AC8 PRO D 97 GLY D 103 1 7 HELIX 27 AC9 ASN D 106 ALA D 111 1 6 HELIX 28 AD1 ALA D 111 LEU D 125 1 15 SHEET 1 AA1 4 TRP A 79 LEU A 85 0 SHEET 2 AA1 4 PHE A 88 TYR A 94 -1 O TYR A 94 N TRP A 79 SHEET 3 AA1 4 ILE A 145 GLY A 150 -1 O ILE A 145 N HIS A 93 SHEET 4 AA1 4 HIS A 132 GLN A 135 -1 N HIS A 132 O GLY A 150 SHEET 1 AA2 4 TRP B 79 LEU B 85 0 SHEET 2 AA2 4 PHE B 88 TYR B 94 -1 O TYR B 94 N TRP B 79 SHEET 3 AA2 4 ILE B 145 GLY B 150 -1 O ILE B 145 N HIS B 93 SHEET 4 AA2 4 HIS B 132 GLN B 135 -1 N HIS B 132 O GLY B 150 SHEET 1 AA3 4 TRP C 79 LEU C 85 0 SHEET 2 AA3 4 PHE C 88 TYR C 94 -1 O TYR C 94 N TRP C 79 SHEET 3 AA3 4 ILE C 145 GLY C 150 -1 O ILE C 145 N HIS C 93 SHEET 4 AA3 4 HIS C 132 GLN C 135 -1 N HIS C 132 O GLY C 150 SHEET 1 AA4 4 TRP D 79 LEU D 85 0 SHEET 2 AA4 4 PHE D 88 TYR D 94 -1 O TYR D 94 N TRP D 79 SHEET 3 AA4 4 ILE D 145 GLY D 150 -1 O ILE D 145 N HIS D 93 SHEET 4 AA4 4 HIS D 132 GLN D 135 -1 N HIS D 132 O GLY 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