HEADER METAL BINDING PROTEIN 01-NOV-24 9E7J TITLE CU-BOUND TETRAMERIC COPPER STORAGE PROTEIN 1 WITH ANTI-RHODOPSIN 1D4 TITLE 2 EPITOPE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FOUR-HELIX BUNDLE COPPER-BINDING PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOSINUS TRICHOSPORIUM OB3B; SOURCE 3 ORGANISM_TAXID: 595536; SOURCE 4 GENE: CQW49_12740; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TETRAMERIC COPPER STORAGE PROTEIN 1, METAL BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.YAO,A.C.OKEN,D.L.FARRENS REVDAT 2 23-JUL-25 9E7J 1 JRNL REVDAT 1 07-MAY-25 9E7J 0 JRNL AUTH W.YAO,A.C.OKEN,D.L.FARRENS JRNL TITL A NOVEL "BIO-TAG" FOR CRYO-EM STUDIES BASED ON THE SMALL, JRNL TITL 2 ELECTRON-DENSE PROTEIN CSP1. JRNL REF BIOPHYS.J. V. 124 1414 2025 JRNL REFN ESSN 1542-0086 JRNL PMID 40620219 JRNL DOI 10.1016/J.BPJ.2025.03.018 REMARK 2 REMARK 2 RESOLUTION. 2.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, CRYOSPARC, PHENIX, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 5FJE 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 : 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) : 2.980 REMARK 3 NUMBER OF PARTICLES : 125008 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 9E7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1000289720. 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 : CU-BOUND TETRAMERIC COPPER REMARK 245 STORAGE PROTEIN 1 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 : 7020 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1700.00 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) : 4200.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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 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 PHE A 75 31.32 -99.46 REMARK 500 PHE B 75 31.32 -99.46 REMARK 500 PHE C 75 31.32 -99.46 REMARK 500 PHE D 75 31.32 -99.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-47678 RELATED DB: EMDB REMARK 900 CU-BOUND TETRAMERIC COPPER STORAGE PROTEIN 1 WITH ANTI-RHODOPSIN REMARK 900 1D4 EPITOPE DBREF1 9E7J A 13 122 UNP A0A2D2D105_METTR DBREF2 9E7J A A0A2D2D105 37 146 DBREF1 9E7J B 13 122 UNP A0A2D2D105_METTR DBREF2 9E7J B A0A2D2D105 37 146 DBREF1 9E7J C 13 122 UNP A0A2D2D105_METTR DBREF2 9E7J C A0A2D2D105 37 146 DBREF1 9E7J D 13 122 UNP A0A2D2D105_METTR DBREF2 9E7J D A0A2D2D105 37 146 SEQRES 1 A 110 GLY ALA LYS TYR LYS ALA LEU LEU ASP SER SER SER HIS SEQRES 2 A 110 CYS VAL ALA VAL GLY GLU ASP CYS LEU ARG HIS CYS PHE SEQRES 3 A 110 GLU MET LEU ALA MET ASN ASP ALA SER MET GLY ALA CYS SEQRES 4 A 110 THR LYS ALA THR TYR ASP LEU VAL ALA ALA CYS GLY ALA SEQRES 5 A 110 LEU ALA LYS LEU ALA GLY THR ASN SER ALA PHE THR PRO SEQRES 6 A 110 ALA PHE ALA LYS VAL VAL ALA ASP VAL CYS ALA ALA CYS SEQRES 7 A 110 LYS LYS GLU CYS ASP LYS PHE PRO SER ILE ALA GLU CYS SEQRES 8 A 110 LYS ALA CYS GLY GLU ALA CYS GLN ALA CYS ALA GLU GLU SEQRES 9 A 110 CYS HIS LYS VAL ALA ALA SEQRES 1 B 110 GLY ALA LYS TYR LYS ALA LEU LEU ASP SER SER SER HIS SEQRES 2 B 110 CYS VAL ALA VAL GLY GLU ASP CYS LEU ARG HIS CYS PHE SEQRES 3 B 110 GLU MET LEU ALA MET ASN ASP ALA SER MET GLY ALA CYS SEQRES 4 B 110 THR LYS ALA THR TYR ASP LEU VAL ALA ALA CYS GLY ALA SEQRES 5 B 110 LEU ALA LYS LEU ALA GLY THR ASN SER ALA PHE THR PRO SEQRES 6 B 110 ALA PHE ALA LYS VAL VAL ALA ASP VAL CYS ALA ALA CYS SEQRES 7 B 110 LYS LYS GLU CYS ASP LYS PHE PRO SER ILE ALA GLU CYS SEQRES 8 B 110 LYS ALA CYS GLY GLU ALA CYS GLN ALA CYS ALA GLU GLU SEQRES 9 B 110 CYS HIS LYS VAL ALA ALA SEQRES 1 C 110 GLY ALA LYS TYR LYS ALA LEU LEU ASP SER SER SER HIS SEQRES 2 C 110 CYS VAL ALA VAL GLY GLU ASP CYS LEU ARG HIS CYS PHE SEQRES 3 C 110 GLU MET LEU ALA MET ASN ASP ALA SER MET GLY ALA CYS SEQRES 4 C 110 THR LYS ALA THR TYR ASP LEU VAL ALA ALA CYS GLY ALA SEQRES 5 C 110 LEU ALA LYS LEU ALA GLY THR ASN SER ALA PHE THR PRO SEQRES 6 C 110 ALA PHE ALA LYS VAL VAL ALA ASP VAL CYS ALA ALA CYS SEQRES 7 C 110 LYS LYS GLU CYS ASP LYS PHE PRO SER ILE ALA GLU CYS SEQRES 8 C 110 LYS ALA CYS GLY GLU ALA CYS GLN ALA CYS ALA GLU GLU SEQRES 9 C 110 CYS HIS LYS VAL ALA ALA SEQRES 1 D 110 GLY ALA LYS TYR LYS ALA LEU LEU ASP SER SER SER HIS SEQRES 2 D 110 CYS VAL ALA VAL GLY GLU ASP CYS LEU ARG HIS CYS PHE SEQRES 3 D 110 GLU MET LEU ALA MET ASN ASP ALA SER MET GLY ALA CYS SEQRES 4 D 110 THR LYS ALA THR TYR ASP LEU VAL ALA ALA CYS GLY ALA SEQRES 5 D 110 LEU ALA LYS LEU ALA GLY THR ASN SER ALA PHE THR PRO SEQRES 6 D 110 ALA PHE ALA LYS VAL VAL ALA ASP VAL CYS ALA ALA CYS SEQRES 7 D 110 LYS LYS GLU CYS ASP LYS PHE PRO SER ILE ALA GLU CYS SEQRES 8 D 110 LYS ALA CYS GLY GLU ALA CYS GLN ALA CYS ALA GLU GLU SEQRES 9 D 110 CYS HIS LYS VAL ALA ALA HELIX 1 AA1 TYR A 16 ALA A 42 1 27 HELIX 2 AA2 MET A 48 THR A 71 1 24 HELIX 3 AA3 PHE A 75 ASP A 95 1 21 HELIX 4 AA4 ILE A 100 ALA A 122 1 23 HELIX 5 AA5 TYR B 16 ALA B 42 1 27 HELIX 6 AA6 MET B 48 THR B 71 1 24 HELIX 7 AA7 PHE B 75 ASP B 95 1 21 HELIX 8 AA8 ILE B 100 ALA B 122 1 23 HELIX 9 AA9 TYR C 16 ALA C 42 1 27 HELIX 10 AB1 MET C 48 THR C 71 1 24 HELIX 11 AB2 PHE C 75 ASP C 95 1 21 HELIX 12 AB3 ILE C 100 ALA C 122 1 23 HELIX 13 AB4 TYR D 16 ALA D 42 1 27 HELIX 14 AB5 MET D 48 THR D 71 1 24 HELIX 15 AB6 PHE D 75 ASP D 95 1 21 HELIX 16 AB7 ILE D 100 ALA D 122 1 23 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 TER 779 ALA A 122 TER 1558 ALA B 122 TER 2337 ALA C 122 TER 3116 ALA D 122 MASTER 124 0 0 16 0 0 0 6 3112 4 0 36 END