HEADER METAL BINDING PROTEIN 09-FEB-16 5I2Q TITLE STRUCTURE OF EF-HAND CONTAINING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: EF-HAND DOMAIN-CONTAINING PROTEIN D2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 70-184; COMPND 5 SYNONYM: SWIPROSIN-1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: EFHD2, SWS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS CALCIUM BINDING PROTEIN, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.R.PARK,M.S.KWON,J.Y.AN,J.G.LEE,H.S.YOUN,Y.LEE,J.Y.KANG,T.G.KIM, AUTHOR 2 J.J.LIM,J.S.PARK,S.H.LEE,W.K.SONG,H.CHEONG,C.JUN,S.H.EOM REVDAT 2 08-NOV-23 5I2Q 1 LINK REVDAT 1 28-DEC-16 5I2Q 0 JRNL AUTH K.R.PARK,M.S.KWON,J.Y.AN,J.G.LEE,H.S.YOUN,Y.LEE,J.Y.KANG, JRNL AUTH 2 T.G.KIM,J.J.LIM,J.S.PARK,S.H.LEE,W.K.SONG,H.K.CHEONG, JRNL AUTH 3 C.D.JUN,S.H.EOM JRNL TITL STRUCTURAL IMPLICATIONS OF CA(2+)-DEPENDENT ACTIN-BUNDLING JRNL TITL 2 FUNCTION OF HUMAN EFHD2/SWIPROSIN-1. JRNL REF SCI REP V. 6 39095 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27974828 JRNL DOI 10.1038/SREP39095 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 7905 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.450 REMARK 3 FREE R VALUE TEST SET COUNT : 352 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 29.3969 - 2.7905 0.98 2625 135 0.1671 0.1750 REMARK 3 2 2.7905 - 2.2151 1.00 2537 114 0.1855 0.2460 REMARK 3 3 2.2151 - 1.9352 0.95 2391 103 0.1655 0.2468 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.009 862 REMARK 3 ANGLE : 1.020 1147 REMARK 3 CHIRALITY : 0.079 122 REMARK 3 PLANARITY : 0.003 148 REMARK 3 DIHEDRAL : 14.597 336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 80 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.7432 -7.2644 4.1851 REMARK 3 T TENSOR REMARK 3 T11: 0.0929 T22: 0.1019 REMARK 3 T33: 0.0967 T12: -0.0542 REMARK 3 T13: -0.0047 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.1263 L22: 0.1065 REMARK 3 L33: 0.0739 L12: -0.1139 REMARK 3 L13: -0.0804 L23: 0.0746 REMARK 3 S TENSOR REMARK 3 S11: -0.0725 S12: 0.0320 S13: -0.0501 REMARK 3 S21: -0.0450 S22: 0.0441 S23: 0.1134 REMARK 3 S31: 0.0705 S32: -0.0148 S33: -0.0097 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 114 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.0283 4.2810 -3.1091 REMARK 3 T TENSOR REMARK 3 T11: 0.1173 T22: 0.1367 REMARK 3 T33: 0.1219 T12: -0.0050 REMARK 3 T13: 0.0107 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 0.0605 L22: 0.0379 REMARK 3 L33: 0.0215 L12: 0.0447 REMARK 3 L13: -0.0133 L23: 0.0006 REMARK 3 S TENSOR REMARK 3 S11: -0.0921 S12: 0.0882 S13: 0.0984 REMARK 3 S21: -0.0656 S22: 0.1550 S23: -0.0388 REMARK 3 S31: 0.0911 S32: -0.0511 S33: 0.0008 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 150 THROUGH 184 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.6304 1.9822 9.3568 REMARK 3 T TENSOR REMARK 3 T11: 0.0909 T22: 0.0861 REMARK 3 T33: 0.1037 T12: -0.0235 REMARK 3 T13: 0.0199 T23: -0.0161 REMARK 3 L TENSOR REMARK 3 L11: 0.0204 L22: 0.0197 REMARK 3 L33: 0.0159 L12: -0.0105 REMARK 3 L13: 0.0060 L23: -0.0046 REMARK 3 S TENSOR REMARK 3 S11: 0.0283 S12: -0.1157 S13: 0.0036 REMARK 3 S21: 0.0105 S22: -0.0141 S23: 0.0300 REMARK 3 S31: -0.0203 S32: -0.0765 S33: -0.0012 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 5I2Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218158. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 95 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 : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7948 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.27100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.8_1069 REMARK 200 STARTING MODEL: 5I2L REMARK 200 REMARK 200 REMARK: ROD SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH8.5, 23 % PEG 2000, REMARK 280 VAPOR DIFFUSION, 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 17.79900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.66700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.05350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.66700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.79900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.05350 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 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 65 REMARK 465 ALA A 66 REMARK 465 MET A 67 REMARK 465 GLY A 68 REMARK 465 SER A 69 REMARK 465 GLY A 70 REMARK 465 GLU A 71 REMARK 465 PRO A 72 REMARK 465 GLN A 73 REMARK 465 SER A 74 REMARK 465 PRO A 75 REMARK 465 SER A 76 REMARK 465 ARG A 77 REMARK 465 ARG A 78 REMARK 465 VAL A 79 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 SER A 183 30.84 -98.50 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 105 OD1 REMARK 620 2 ASP A 109 OD1 78.9 REMARK 620 3 PHE A 111 O 78.9 86.0 REMARK 620 4 GLU A 116 OE1 115.7 156.8 79.8 REMARK 620 5 GLU A 116 OE2 87.3 149.9 117.7 52.8 REMARK 620 6 HOH A 320 O 157.6 79.8 92.7 82.6 114.8 REMARK 620 7 HOH A 355 O 111.0 80.6 161.2 108.2 79.6 72.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5I2L RELATED DB: PDB REMARK 900 RELATED ID: 5I2O RELATED DB: PDB DBREF 5I2Q A 70 184 UNP Q96C19 EFHD2_HUMAN 70 184 SEQADV 5I2Q GLY A 65 UNP Q96C19 EXPRESSION TAG SEQADV 5I2Q ALA A 66 UNP Q96C19 EXPRESSION TAG SEQADV 5I2Q MET A 67 UNP Q96C19 EXPRESSION TAG SEQADV 5I2Q GLY A 68 UNP Q96C19 EXPRESSION TAG SEQADV 5I2Q SER A 69 UNP Q96C19 EXPRESSION TAG SEQADV 5I2Q ALA A 152 UNP Q96C19 GLU 152 ENGINEERED MUTATION SEQRES 1 A 120 GLY ALA MET GLY SER GLY GLU PRO GLN SER PRO SER ARG SEQRES 2 A 120 ARG VAL PHE ASN PRO TYR THR GLU PHE LYS GLU PHE SER SEQRES 3 A 120 ARG LYS GLN ILE LYS ASP MET GLU LYS MET PHE LYS GLN SEQRES 4 A 120 TYR ASP ALA GLY ARG ASP GLY PHE ILE ASP LEU MET GLU SEQRES 5 A 120 LEU LYS LEU MET MET GLU LYS LEU GLY ALA PRO GLN THR SEQRES 6 A 120 HIS LEU GLY LEU LYS ASN MET ILE LYS GLU VAL ASP GLU SEQRES 7 A 120 ASP PHE ASP SER LYS LEU SER PHE ARG ALA PHE LEU LEU SEQRES 8 A 120 ILE PHE ARG LYS ALA ALA ALA GLY GLU LEU GLN GLU ASP SEQRES 9 A 120 SER GLY LEU CYS VAL LEU ALA ARG LEU SER GLU ILE ASP SEQRES 10 A 120 VAL SER SER HET CA A 201 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *62(H2 O) HELIX 1 AA1 ASN A 81 PHE A 86 1 6 HELIX 2 AA2 SER A 90 ASP A 105 1 16 HELIX 3 AA3 ASP A 113 GLY A 125 1 13 HELIX 4 AA4 THR A 129 ASP A 141 1 13 HELIX 5 AA5 SER A 149 ALA A 162 1 14 HELIX 6 AA6 SER A 169 SER A 178 1 10 LINK OD1 ASP A 105 CA CA A 201 1555 1555 2.32 LINK OD1 ASP A 109 CA CA A 201 1555 1555 2.34 LINK O PHE A 111 CA CA A 201 1555 1555 2.34 LINK OE1 GLU A 116 CA CA A 201 1555 1555 2.49 LINK OE2 GLU A 116 CA CA A 201 1555 1555 2.51 LINK CA CA A 201 O HOH A 320 1555 1555 2.56 LINK CA CA A 201 O HOH A 355 1555 1555 2.61 SITE 1 AC1 6 ASP A 105 ASP A 109 PHE A 111 GLU A 116 SITE 2 AC1 6 HOH A 320 HOH A 355 CRYST1 35.598 52.107 55.334 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 0.028091 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018072 0.00000