HEADER METAL BINDING PROTEIN 15-AUG-11 3TER TITLE CRYSTAL STRUCTURE OF SOAR DOMAIN WITH INHIBITION HELIX FROM C. ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAMMALIAN STROMAL INTERACTION MOLECULE-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 256-391; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: STIM-1, Y55B1BM.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS DIMER, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.YANG,H.JIN,X.CAI,Y.SHEN REVDAT 3 20-MAR-24 3TER 1 REMARK REVDAT 2 10-JUL-13 3TER 1 JRNL REVDAT 1 11-APR-12 3TER 0 JRNL AUTH X.YANG,H.JIN,X.CAI,S.LI,Y.SHEN JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO THE ACTIVATION OF JRNL TITL 2 STROMAL INTERACTION MOLECULE 1 (STIM1). JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 5657 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22451904 JRNL DOI 10.1073/PNAS.1118947109 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.3 REMARK 3 NUMBER OF REFLECTIONS : 10161 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1156 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 29.6456 - 5.0940 0.72 1127 132 0.2400 0.2876 REMARK 3 2 5.0940 - 4.0466 0.83 1293 139 0.1430 0.2033 REMARK 3 3 4.0466 - 3.5360 0.85 1357 151 0.1632 0.2452 REMARK 3 4 3.5360 - 3.2131 0.87 1353 150 0.1724 0.2579 REMARK 3 5 3.2131 - 2.9830 0.86 1358 161 0.2072 0.3028 REMARK 3 6 2.9830 - 2.8073 0.83 1299 156 0.2268 0.2951 REMARK 3 7 2.8073 - 2.6668 0.80 1252 138 0.2509 0.3397 REMARK 3 8 2.6668 - 2.5508 0.75 1176 129 0.2854 0.3416 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 81.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.620 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) : -2.79510 REMARK 3 B22 (A**2) : -2.79510 REMARK 3 B33 (A**2) : 5.59030 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.008 1914 REMARK 3 ANGLE : 1.152 2562 REMARK 3 CHIRALITY : 0.076 293 REMARK 3 PLANARITY : 0.004 335 REMARK 3 DIHEDRAL : 20.267 746 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -19.0184 -11.4072 9.0294 REMARK 3 T TENSOR REMARK 3 T11: 0.3396 T22: 0.3009 REMARK 3 T33: 0.4479 T12: 0.0099 REMARK 3 T13: -0.0026 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 2.0548 L22: 1.5149 REMARK 3 L33: 0.1206 L12: -0.0536 REMARK 3 L13: -0.1311 L23: -0.1913 REMARK 3 S TENSOR REMARK 3 S11: -0.1851 S12: -0.1543 S13: 0.1842 REMARK 3 S21: -0.2173 S22: 0.0240 S23: 0.0459 REMARK 3 S31: 0.0473 S32: 0.0235 S33: 0.1566 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 3TER COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067391. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-11; 09-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SSRF; SSRF REMARK 200 BEAMLINE : BL17U; BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791; 0.9791 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; SI 111 CHANNEL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R; ADSC QUANTUM REMARK 200 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10722 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.0, 15% TACSIMATE PH REMARK 280 7.0, 2% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.19800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.59900 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 256 REMARK 465 VAL A 257 REMARK 465 ALA A 279 REMARK 465 ASN A 280 REMARK 465 SER A 281 REMARK 465 ASN A 282 REMARK 465 GLY A 283 REMARK 465 GLN A 330 REMARK 465 GLY A 331 REMARK 465 SER A 332 REMARK 465 VAL A 333 REMARK 465 LEU A 334 REMARK 465 SER A 335 REMARK 465 TYR A 388 REMARK 465 LEU A 389 REMARK 465 ASN A 390 REMARK 465 GLU A 391 REMARK 465 GLY B 256 REMARK 465 VAL B 257 REMARK 465 VAL B 258 REMARK 465 ALA B 279 REMARK 465 ASN B 280 REMARK 465 SER B 281 REMARK 465 GLN B 330 REMARK 465 GLY B 331 REMARK 465 SER B 332 REMARK 465 VAL B 333 REMARK 465 LEU B 334 REMARK 465 SER B 335 REMARK 465 LEU B 389 REMARK 465 ASN B 390 REMARK 465 GLU B 391 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 258 CG1 CG2 REMARK 470 ASN A 259 CG OD1 ND2 REMARK 470 SER A 284 OG REMARK 470 LYS A 329 CG CD CE NZ REMARK 470 SER A 336 OG REMARK 470 LEU A 337 CG CD1 CD2 REMARK 470 LYS A 338 CG CD CE NZ REMARK 470 LEU A 339 CG CD1 CD2 REMARK 470 THR A 341 OG1 CG2 REMARK 470 ASN B 259 CG OD1 ND2 REMARK 470 ARG B 267 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 282 CG OD1 ND2 REMARK 470 LYS B 329 CG CD CE NZ REMARK 470 SER B 336 OG REMARK 470 LEU B 337 CG CD1 CD2 REMARK 470 LYS B 338 CG CD CE NZ REMARK 470 LEU B 339 CG CD1 CD2 REMARK 470 THR B 341 OG1 CG2 REMARK 470 TYR B 388 CG CD1 CD2 CE1 CE2 CZ OH 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 ASN A 259 -110.62 -121.26 REMARK 500 HIS A 260 -138.08 49.84 REMARK 500 LYS A 328 -90.06 -58.49 REMARK 500 LYS A 338 -149.49 -101.82 REMARK 500 ALA A 340 -2.57 81.09 REMARK 500 THR A 341 -147.60 83.97 REMARK 500 ALA A 343 -151.01 -134.40 REMARK 500 LEU A 386 -17.66 -148.57 REMARK 500 HIS B 260 -67.99 -170.71 REMARK 500 LYS B 328 -86.76 -60.34 REMARK 500 LYS B 338 -152.78 84.22 REMARK 500 ALA B 340 -14.82 90.62 REMARK 500 THR B 341 -145.86 83.66 REMARK 500 ALA B 343 -161.83 -122.43 REMARK 500 LEU B 386 -24.22 -158.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 3TER A 256 391 UNP Q9N379 Q9N379_CAEEL 256 391 DBREF 3TER B 256 391 UNP Q9N379 Q9N379_CAEEL 256 391 SEQRES 1 A 136 GLY VAL VAL ASN HIS THR GLU MET GLU ASN LEU ARG VAL SEQRES 2 A 136 GLN LEU GLU GLU ALA GLU ARG ARG LEU GLU ALA ASN SER SEQRES 3 A 136 ASN GLY SER GLN ALA PRO LEU ALA LEU GLN PRO LEU LEU SEQRES 4 A 136 ARG ARG THR CYS GLU ASN GLU MET ALA PHE LEU GLU LYS SEQRES 5 A 136 GLN ARG GLN ASP CYS PHE LYS GLU MET LYS GLU ALA ILE SEQRES 6 A 136 GLU MET VAL ASP ARG LEU GLN LYS LYS GLN GLY SER VAL SEQRES 7 A 136 LEU SER SER LEU LYS LEU ALA THR GLY ALA ALA SER THR SEQRES 8 A 136 SER ASP GLN VAL ASP SER LYS ILE PHE ALA LEU LYS SER SEQRES 9 A 136 ARG MET GLU LYS ILE HIS THR LEU THR ARG GLU THR GLN SEQRES 10 A 136 GLU ARG TRP LEU GLN ILE GLU SER LEU CYS GLY PHE PRO SEQRES 11 A 136 LEU LEU TYR LEU ASN GLU SEQRES 1 B 136 GLY VAL VAL ASN HIS THR GLU MET GLU ASN LEU ARG VAL SEQRES 2 B 136 GLN LEU GLU GLU ALA GLU ARG ARG LEU GLU ALA ASN SER SEQRES 3 B 136 ASN GLY SER GLN ALA PRO LEU ALA LEU GLN PRO LEU LEU SEQRES 4 B 136 ARG ARG THR CYS GLU ASN GLU MET ALA PHE LEU GLU LYS SEQRES 5 B 136 GLN ARG GLN ASP CYS PHE LYS GLU MET LYS GLU ALA ILE SEQRES 6 B 136 GLU MET VAL ASP ARG LEU GLN LYS LYS GLN GLY SER VAL SEQRES 7 B 136 LEU SER SER LEU LYS LEU ALA THR GLY ALA ALA SER THR SEQRES 8 B 136 SER ASP GLN VAL ASP SER LYS ILE PHE ALA LEU LYS SER SEQRES 9 B 136 ARG MET GLU LYS ILE HIS THR LEU THR ARG GLU THR GLN SEQRES 10 B 136 GLU ARG TRP LEU GLN ILE GLU SER LEU CYS GLY PHE PRO SEQRES 11 B 136 LEU LEU TYR LEU ASN GLU FORMUL 3 HOH *32(H2 O) HELIX 1 1 ASN A 259 GLU A 278 1 20 HELIX 2 2 ALA A 289 LYS A 329 1 41 HELIX 3 3 SER A 345 GLY A 383 1 39 HELIX 4 4 THR B 261 GLU B 278 1 18 HELIX 5 5 ALA B 289 LYS B 329 1 41 HELIX 6 6 SER B 345 GLY B 383 1 39 CISPEP 1 ASN B 259 HIS B 260 0 -2.89 CRYST1 76.988 76.988 64.797 90.00 90.00 120.00 P 32 6 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 0.012989 0.007499 0.000000 0.00000 SCALE2 0.000000 0.014998 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015433 0.00000