HEADER METAL BINDING PROTEIN 12-JUL-22 7YGV TITLE CRYSTAL STRUCTURE OF THE CA2+-BOUND EFHD1/SWIPROSIN-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EF-HAND DOMAIN-CONTAINING PROTEIN D1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EF-HAND DOMAIN-CONTAINING PROTEIN 1,MITOCALCIN,SWIPROSIN-2; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: [GAMGS + EFHD1(69-193)](GAMGS: THE CLEAVED SITE AFTER COMPND 7 GST-TEV TAG CLEAVAGE) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: EFHD1, SWS2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS MITOCHONDRIA, EF-HAND CONTAINING PROTEIN, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.A.MUN,J.PARK,J.Y.KANG,T.PARK,M.JIN,J.YNAG,S.H.EOM REVDAT 1 15-MAR-23 7YGV 0 JRNL AUTH S.A.MUN,J.PARK,J.Y.KANG,T.PARK,M.JIN,J.YANG,S.H.EOM JRNL TITL STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO ZN 2+ -BOUND JRNL TITL 2 EF-HAND PROTEINS, EFHD1 AND EFHD2. JRNL REF IUCRJ V. 10 233 2023 JRNL REFN ESSN 2052-2525 JRNL PMID 36862489 JRNL DOI 10.1107/S2052252523001501 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1-4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 6072 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.880 REMARK 3 FREE R VALUE TEST SET COUNT : 600 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.7200 - 4.4500 0.94 1359 162 0.1832 0.2518 REMARK 3 2 4.4400 - 3.5300 1.00 1443 158 0.1864 0.2291 REMARK 3 3 3.5300 - 3.0800 0.99 1439 157 0.2016 0.3122 REMARK 3 4 3.0800 - 2.8000 0.84 1231 123 0.2435 0.2323 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.311 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.817 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 848 REMARK 3 ANGLE : 1.039 1130 REMARK 3 CHIRALITY : 0.056 119 REMARK 3 PLANARITY : 0.006 145 REMARK 3 DIHEDRAL : 17.441 325 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7YGV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28255 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3596 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 22.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1-4487 REMARK 200 STARTING MODEL: 7CLT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.5, 0.4 MM ZNSO4, REMARK 280 AND 25% (W/V) JEFFAMINE ED-2001, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 22.12550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.71700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.95350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.71700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.12550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.95350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 70 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL 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 GLY A 64 REMARK 465 ALA A 65 REMARK 465 MET A 66 REMARK 465 GLY A 67 REMARK 465 SER A 68 REMARK 465 GLY A 69 REMARK 465 THR A 70 REMARK 465 ALA A 71 REMARK 465 ARG A 72 REMARK 465 PRO A 73 REMARK 465 GLY A 74 REMARK 465 ARG A 75 REMARK 465 SER A 76 REMARK 465 LYS A 77 REMARK 465 VAL A 78 REMARK 465 VAL A 181 REMARK 465 ALA A 182 REMARK 465 LEU A 183 REMARK 465 GLU A 184 REMARK 465 GLY A 185 REMARK 465 VAL A 186 REMARK 465 ARG A 187 REMARK 465 GLY A 188 REMARK 465 ALA A 189 REMARK 465 LYS A 190 REMARK 465 ASN A 191 REMARK 465 PHE A 192 REMARK 465 PHE A 193 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 178 18.55 57.70 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 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 104 OD1 REMARK 620 2 ASP A 108 OD1 78.4 REMARK 620 3 PHE A 110 O 69.6 77.0 REMARK 620 4 GLU A 115 OE1 109.0 144.3 73.6 REMARK 620 5 GLU A 115 OE2 89.7 162.0 111.8 52.6 REMARK 620 6 HOH A 309 O 139.9 70.7 78.8 84.1 125.6 REMARK 620 7 HOH A 312 O 105.3 97.1 172.7 113.4 72.8 103.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 129 NE2 REMARK 620 2 LYS A 133 NZ 126.6 REMARK 620 3 HIS A 157 NE2 80.5 49.1 REMARK 620 4 GLU A 163 OE1 78.9 48.8 6.9 REMARK 620 5 GLU A 163 OE2 81.9 45.4 9.6 4.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 140 OD1 REMARK 620 2 ASP A 142 OD1 82.9 REMARK 620 3 ASP A 144 OD1 81.3 81.0 REMARK 620 4 LYS A 146 O 83.7 152.3 73.0 REMARK 620 5 GLU A 151 OE1 103.4 126.6 152.2 80.2 REMARK 620 6 GLU A 151 OE2 84.4 78.2 156.1 124.4 50.6 REMARK 620 7 HOH A 302 O 156.1 80.4 79.2 103.7 100.3 108.6 REMARK 620 N 1 2 3 4 5 6 DBREF 7YGV A 69 193 UNP Q9D4J1 EFHD1_MOUSE 69 193 SEQADV 7YGV GLY A 64 UNP Q9D4J1 EXPRESSION TAG SEQADV 7YGV ALA A 65 UNP Q9D4J1 EXPRESSION TAG SEQADV 7YGV MET A 66 UNP Q9D4J1 EXPRESSION TAG SEQADV 7YGV GLY A 67 UNP Q9D4J1 EXPRESSION TAG SEQADV 7YGV SER A 68 UNP Q9D4J1 EXPRESSION TAG SEQRES 1 A 130 GLY ALA MET GLY SER GLY THR ALA ARG PRO GLY ARG SER SEQRES 2 A 130 LYS VAL PHE ASN PRO TYR THR GLU PHE PRO GLU PHE SER SEQRES 3 A 130 ARG ARG LEU LEU LYS ASP LEU GLU LYS MET PHE LYS THR SEQRES 4 A 130 TYR ASP ALA GLY ARG ASP GLY PHE ILE ASP LEU MET GLU SEQRES 5 A 130 LEU LYS LEU MET MET GLU LYS LEU GLY ALA PRO GLN THR SEQRES 6 A 130 HIS LEU GLY LEU LYS SER MET ILE LYS GLU VAL ASP GLU SEQRES 7 A 130 ASP PHE ASP GLY LYS LEU SER PHE ARG GLU PHE LEU LEU SEQRES 8 A 130 ILE PHE HIS LYS ALA ALA ALA GLY GLU LEU GLN GLU ASP SEQRES 9 A 130 SER GLY LEU LEU ALA LEU ALA LYS PHE SER GLU ILE ASP SEQRES 10 A 130 VAL ALA LEU GLU GLY VAL ARG GLY ALA LYS ASN PHE PHE HET CA A 201 1 HET CA A 202 1 HET GOL A 203 6 HET ZN A 204 1 HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CA 2(CA 2+) FORMUL 4 GOL C3 H8 O3 FORMUL 5 ZN ZN 2+ FORMUL 6 HOH *20(H2 O) HELIX 1 AA1 ASN A 80 PHE A 85 1 6 HELIX 2 AA2 SER A 89 ASP A 104 1 16 HELIX 3 AA3 ASP A 112 LEU A 123 1 12 HELIX 4 AA4 THR A 128 ASP A 140 1 13 HELIX 5 AA5 PHE A 149 GLY A 162 1 14 HELIX 6 AA6 SER A 168 SER A 177 1 10 SHEET 1 AA1 2 PHE A 110 ILE A 111 0 SHEET 2 AA1 2 LEU A 147 SER A 148 -1 O LEU A 147 N ILE A 111 LINK OD1 ASP A 104 CA CA A 201 1555 1555 2.16 LINK OD1 ASP A 108 CA CA A 201 1555 1555 2.47 LINK O PHE A 110 CA CA A 201 1555 1555 2.52 LINK OE1 GLU A 115 CA CA A 201 1555 1555 2.53 LINK OE2 GLU A 115 CA CA A 201 1555 1555 2.42 LINK NE2 HIS A 129 ZN ZN A 204 1555 1555 2.24 LINK NZ LYS A 133 ZN ZN A 204 1555 1555 2.27 LINK OD1 ASP A 140 CA CA A 202 1555 1555 2.34 LINK OD1 ASP A 142 CA CA A 202 1555 1555 2.32 LINK OD1 ASP A 144 CA CA A 202 1555 1555 2.40 LINK O LYS A 146 CA CA A 202 1555 1555 2.51 LINK OE1 GLU A 151 CA CA A 202 1555 1555 2.50 LINK OE2 GLU A 151 CA CA A 202 1555 1555 2.67 LINK NE2 HIS A 157 ZN ZN A 204 1555 3745 2.29 LINK OE1 GLU A 163 ZN ZN A 204 1555 3745 2.28 LINK OE2 GLU A 163 ZN ZN A 204 1555 3745 2.48 LINK CA CA A 201 O HOH A 309 1555 1555 2.33 LINK CA CA A 201 O HOH A 312 1555 1555 2.26 LINK CA CA A 202 O HOH A 302 1555 1555 2.20 CRYST1 44.251 47.907 63.434 90.00 90.00 90.00 P 21 21 21 4 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 0.022598 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020874 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015764 0.00000