HEADER PROTEIN BINDING 12-NOV-19 6UY7 TITLE CRYSTAL STRUCTURE OF THE STAC3 TANDEM SH3 DOMAINS - P269R COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH3 AND CYSTEINE-RICH DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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: STAC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN BINDING DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.RUFENACH,F.VAN PETEGEM REVDAT 3 11-OCT-23 6UY7 1 REMARK REVDAT 2 19-AUG-20 6UY7 1 JRNL REVDAT 1 17-JUN-20 6UY7 0 JRNL AUTH B.RUFENACH,D.CHRISTY,B.E.FLUCHER,J.M.BUI,J.GSPONER, JRNL AUTH 2 M.CAMPIGLIO,F.VAN PETEGEM JRNL TITL MULTIPLE SEQUENCE VARIANTS IN STAC3 AFFECT INTERACTIONS WITH JRNL TITL 2 CAV1.1 AND EXCITATION-CONTRACTION COUPLING. JRNL REF STRUCTURE V. 28 922 2020 JRNL REFN ISSN 0969-2126 JRNL PMID 32492370 JRNL DOI 10.1016/J.STR.2020.05.005 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.1_3469 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 7350 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.510 REMARK 3 FREE R VALUE TEST SET COUNT : 405 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 38.0210 - 3.0358 1.00 2433 164 0.2025 0.2568 REMARK 3 2 3.0358 - 2.4097 1.00 2366 138 0.2467 0.3013 REMARK 3 3 2.4097 - 2.1052 0.90 2146 103 0.2476 0.2986 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 31.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.14 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 250 THROUGH 304 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.8720 -31.0559 -5.0694 REMARK 3 T TENSOR REMARK 3 T11: 0.1536 T22: 0.1629 REMARK 3 T33: 0.0634 T12: -0.0996 REMARK 3 T13: -0.0416 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 3.9435 L22: 4.5039 REMARK 3 L33: 2.0998 L12: -1.2273 REMARK 3 L13: -1.8179 L23: 1.0023 REMARK 3 S TENSOR REMARK 3 S11: 0.0544 S12: -0.2406 S13: 0.1423 REMARK 3 S21: 0.2615 S22: -0.0709 S23: -0.4275 REMARK 3 S31: -0.2871 S32: 0.2502 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 305 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.4959 -49.9533 -10.9363 REMARK 3 T TENSOR REMARK 3 T11: 0.3069 T22: 0.3661 REMARK 3 T33: 0.8015 T12: 0.0192 REMARK 3 T13: 0.2345 T23: 0.1212 REMARK 3 L TENSOR REMARK 3 L11: 3.8949 L22: 2.6876 REMARK 3 L33: 1.8503 L12: -1.2261 REMARK 3 L13: -1.9696 L23: -0.0696 REMARK 3 S TENSOR REMARK 3 S11: -0.4395 S12: -0.2170 S13: -1.3982 REMARK 3 S21: -0.0251 S22: -0.1617 S23: -0.4832 REMARK 3 S31: 0.6115 S32: 0.2155 S33: 0.6062 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 6UY7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000245378. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0331 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7350 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.105 REMARK 200 RESOLUTION RANGE LOW (A) : 38.021 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 60.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6B26, 6B29 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% PEG8000, 100MM MES, 8% ETHYLENE REMARK 280 GLYCOL, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 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 19.22333 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 9.61167 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.22333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 9.61167 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 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 245 REMARK 465 PHE A 246 REMARK 465 GLN A 247 REMARK 465 GLN A 248 REMARK 465 SER A 249 REMARK 465 ARG A 321 REMARK 465 GLU A 322 REMARK 465 ILE A 323 REMARK 465 GLY A 324 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 LEU A 261 CG CD1 CD2 REMARK 470 GLU A 262 CG CD OE1 OE2 REMARK 470 LYS A 288 CG CD CE NZ REMARK 470 GLU A 291 CG CD OE1 OE2 REMARK 470 LYS A 292 CG CD CE NZ REMARK 470 ARG A 303 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 305 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 308 CG CD OE1 OE2 REMARK 470 ARG A 315 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 318 CG1 CG2 REMARK 470 ASN A 320 CG OD1 ND2 REMARK 470 LYS A 329 CG CD CE NZ REMARK 470 ASP A 331 CG OD1 OD2 REMARK 470 GLU A 340 CG CD OE1 OE2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 LYS A 352 CG CD CE NZ REMARK 470 VAL A 353 CG1 CG2 REMARK 470 PHE A 360 CG CD1 CD2 CE1 CE2 CZ 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 ALA A 341 120.75 -173.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 402 DBREF 6UY7 A 245 364 UNP Q96MF2 STAC3_HUMAN 245 364 SEQADV 6UY7 ARG A 269 UNP Q96MF2 PRO 269 ENGINEERED MUTATION SEQRES 1 A 120 GLY PHE GLN GLN SER HIS TYR PHE VAL ALA LEU TYR ARG SEQRES 2 A 120 PHE LYS ALA LEU GLU LYS ASP ASP LEU ASP PHE ARG PRO SEQRES 3 A 120 GLY GLU LYS ILE THR VAL ILE ASP ASP SER ASN GLU GLU SEQRES 4 A 120 TRP TRP ARG GLY LYS ILE GLY GLU LYS VAL GLY PHE PHE SEQRES 5 A 120 PRO PRO ASN PHE ILE ILE ARG VAL ARG ALA GLY GLU ARG SEQRES 6 A 120 VAL HIS ARG VAL THR ARG SER PHE VAL GLY ASN ARG GLU SEQRES 7 A 120 ILE GLY GLN ILE THR LEU LYS LYS ASP GLN ILE VAL VAL SEQRES 8 A 120 GLN LYS GLY ASP GLU ALA GLY GLY TYR VAL LYS VAL TYR SEQRES 9 A 120 THR GLY ARG LYS VAL GLY LEU PHE PRO THR ASP PHE LEU SEQRES 10 A 120 GLU GLU ILE HET EDO A 401 10 HET EDO A 402 10 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 2(C2 H6 O2) FORMUL 4 HOH *41(H2 O) HELIX 1 AA1 PRO A 297 ASN A 299 5 3 SHEET 1 AA1 5 LYS A 292 PHE A 296 0 SHEET 2 AA1 5 TRP A 285 ILE A 289 -1 N GLY A 287 O GLY A 294 SHEET 3 AA1 5 LYS A 273 ASP A 278 -1 N ASP A 278 O ARG A 286 SHEET 4 AA1 5 TYR A 251 ALA A 254 -1 N PHE A 252 O ILE A 274 SHEET 5 AA1 5 ILE A 301 VAL A 304 -1 O VAL A 304 N TYR A 251 SHEET 1 AA2 5 VAL A 353 PRO A 357 0 SHEET 2 AA2 5 TYR A 344 TYR A 348 -1 N VAL A 347 O GLY A 354 SHEET 3 AA2 5 ILE A 333 ALA A 341 -1 N LYS A 337 O LYS A 346 SHEET 4 AA2 5 VAL A 310 VAL A 313 -1 N HIS A 311 O VAL A 334 SHEET 5 AA2 5 LEU A 361 ILE A 364 -1 O GLU A 362 N ARG A 312 SITE 1 AC1 7 TYR A 256 GLU A 283 TRP A 284 PRO A 297 SITE 2 AC1 7 ASN A 299 HOH A 502 HOH A 535 SITE 1 AC2 3 TYR A 256 PHE A 258 LYS A 259 CRYST1 87.805 87.805 28.835 90.00 90.00 120.00 P 62 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 0.011389 0.006575 0.000000 0.00000 SCALE2 0.000000 0.013151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034680 0.00000