HEADER METAL BINDING PROTEIN 24-OCT-24 9K8B TITLE CRYO-EM STRUCTURE OF MONOMER OF DESIGNED ZINC-INDUCED TETRAHEDRON TITLE 2 CAGE-T32-ZN1-HEHE-34 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAGE-T32-ZN1-HEHE-34; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ZINC-BINDING PROTEIN, METAL BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.N.QU,L.X.CAO REVDAT 1 29-OCT-25 9K8B 0 JRNL AUTH Y.N.QU,L.X.CAO JRNL TITL DE NOVO DESIGN OF METAL ION REGULATED PROTEIN ASSEMBLIES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL 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) : 3.060 REMARK 3 NUMBER OF PARTICLES : 578620 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 9K8B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052918. 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 : CAGE-T32-ZN1-HEHE-34 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 : 7.00 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 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) : 5000.00 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: 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 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 -18 REMARK 465 GLY A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 SER A -8 REMARK 465 SER A -7 REMARK 465 GLY A -6 REMARK 465 LEU A -5 REMARK 465 GLU A -4 REMARK 465 VAL A -3 REMARK 465 LEU A -2 REMARK 465 PHE A -1 REMARK 465 GLN A 0 REMARK 465 GLY A 1 REMARK 465 PRO A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 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 GLU A 7 -95.84 77.65 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 32 OD1 REMARK 620 2 HIS A 58 NE2 73.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 OD2 REMARK 620 2 HIS A 166 NE2 79.1 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62167 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF MONOMER OF DESIGNED ZINC-INDUCED TETRAHEDRON REMARK 900 CAGE-T32-ZN1-HEHE-34 DBREF 9K8B A -18 224 PDB 9K8B 9K8B -18 224 SEQRES 1 A 243 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 243 LEU GLU VAL LEU PHE GLN GLY PRO GLY GLY THR MET GLU SEQRES 3 A 243 LYS LEU LYS GLU ILE VAL LYS HIS LEU GLU VAL ALA ILE SEQRES 4 A 243 LYS TYR LEU LYS GLU GLY LYS VAL ASP LEU ALA ASP LEU SEQRES 5 A 243 VAL VAL ALA ASP ALA ILE GLU LEU ALA LYS GLU ALA GLY SEQRES 6 A 243 ASP LYS ALA SER LEU GLU ILE LEU LYS VAL ALA HIS LYS SEQRES 7 A 243 ALA ILE ASP THR LEU GLY ARG GLU GLY LYS LEU GLU GLU SEQRES 8 A 243 ALA ALA LYS ILE VAL LYS TYR ALA LYS GLU TYR VAL GLU SEQRES 9 A 243 ALA LYS ILE LYS GLY ASP ARG GLU LYS LEU ARG GLU LEU SEQRES 10 A 243 LEU GLU LYS VAL LYS LYS ASP VAL LEU GLU ALA ILE LYS SEQRES 11 A 243 LYS GLY ASP GLU GLU PHE TYR GLU ALA LEU VAL LYS ILE SEQRES 12 A 243 ALA ARG ILE ILE ALA GLU ASP LEU GLY ASP GLU LYS SER SEQRES 13 A 243 LEU LYS VAL LEU GLU ALA LEU GLU GLU PHE PHE LYS GLU SEQRES 14 A 243 TRP LYS ARG LEU GLU LYS GLU GLY LYS SER LEU ASP GLU SEQRES 15 A 243 LYS LEU HIS LEU PHE LEU ARG VAL GLY GLU ARG LEU LEU SEQRES 16 A 243 GLU ILE GLY ASP LYS GLU SER LEU GLU MET LEU ILE GLU SEQRES 17 A 243 LEU LEU GLU GLU LEU ALA LYS GLU ILE LYS LYS ALA GLY SEQRES 18 A 243 ASN GLU GLU LEU LEU VAL ARG ALA GLU ALA ALA ILE LYS SEQRES 19 A 243 ASP ILE ARG LYS HIS ILE LYS GLU LEU HET ZN A 301 1 HET ZN A 302 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 GLU A 7 LYS A 24 1 18 HELIX 2 AA2 LYS A 27 LYS A 43 1 17 HELIX 3 AA3 ALA A 49 GLU A 67 1 19 HELIX 4 AA4 ALA A 73 ALA A 86 1 14 HELIX 5 AA5 LYS A 94 GLY A 113 1 20 HELIX 6 AA6 ASP A 114 GLU A 130 1 17 HELIX 7 AA7 LEU A 138 GLU A 157 1 20 HELIX 8 AA8 SER A 160 GLY A 179 1 20 HELIX 9 AA9 LYS A 181 ALA A 201 1 21 HELIX 10 AB1 LEU A 206 LEU A 224 1 19 LINK OD1 ASP A 32 ZN ZN A 301 1555 1555 1.96 LINK NE2 HIS A 58 ZN ZN A 301 1555 1555 2.11 LINK OD2 ASP A 162 ZN ZN A 302 1555 1555 1.98 LINK NE2 HIS A 166 ZN ZN A 302 1555 1555 2.10 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 CONECT 218 1765 CONECT 408 1765 CONECT 1257 1766 CONECT 1293 1766 CONECT 1765 218 408 CONECT 1766 1257 1293 MASTER 165 0 2 10 0 0 0 6 1765 1 6 19 END