HEADER SIGNALING PROTEIN 10-DEC-18 6IXG TITLE CRYSTAL STRUCTURE OF NATIVE APO SH3BP5 (P41) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH3 DOMAIN-BINDING PROTEIN 5; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SH3BP-5,SH3 DOMAIN-BINDING PROTEIN THAT PREFERENTIALLY COMPND 5 ASSOCIATES WITH BTK; 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: SH3BP5, SAB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAB11, GEF, SH3BP5, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.GOTO-ITO,A.YAMAGATA,Y.SATO,S.FUKAI REVDAT 3 22-NOV-23 6IXG 1 REMARK REVDAT 2 27-MAR-19 6IXG 1 JRNL REVDAT 1 20-MAR-19 6IXG 0 JRNL AUTH S.GOTO-ITO,N.MOROOKA,A.YAMAGATA,Y.SATO,K.SATO,S.FUKAI JRNL TITL STRUCTURAL BASIS OF GUANINE NUCLEOTIDE EXCHANGE FOR RAB11 BY JRNL TITL 2 SH3BP5. JRNL REF LIFE SCI ALLIANCE V. 2 2019 JRNL REFN ESSN 2575-1077 JRNL PMID 30872413 JRNL DOI 10.26508/LSA.201900297 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 3.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 5578 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.070 REMARK 3 FREE R VALUE TEST SET COUNT : 227 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 39.9812 - 4.7872 1.00 2838 133 0.2291 0.2632 REMARK 3 2 4.7872 - 3.8007 0.89 2513 94 0.2704 0.3253 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.300 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 : 0.003 3614 REMARK 3 ANGLE : 0.678 4837 REMARK 3 CHIRALITY : 0.026 538 REMARK 3 PLANARITY : 0.004 628 REMARK 3 DIHEDRAL : 11.304 1443 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 6IXG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1300010112. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : 5605 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.800 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 (%) : 94.4 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.18700 REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.87 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.70700 REMARK 200 FOR SHELL : NULL 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: 6IXE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4M MG(NO3)2, 0.1M TRIS-CL PH 8.0, REMARK 280 22% PEG 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.17650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.58825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 70.76475 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 39 REMARK 465 HIS A 40 REMARK 465 SER A 264 REMARK 465 ALA A 265 REMARK 465 MET A 266 REMARK 465 SER B 39 REMARK 465 HIS B 40 REMARK 465 LEU B 144 REMARK 465 GLU B 145 REMARK 465 ASP B 146 REMARK 465 ASP B 147 REMARK 465 LYS B 148 REMARK 465 ARG B 149 REMARK 465 SER B 263 REMARK 465 SER B 264 REMARK 465 ALA B 265 REMARK 465 MET B 266 DBREF 6IXG A 41 266 UNP O60239 3BP5_HUMAN 41 266 DBREF 6IXG B 41 266 UNP O60239 3BP5_HUMAN 41 266 SEQADV 6IXG SER A 39 UNP O60239 EXPRESSION TAG SEQADV 6IXG HIS A 40 UNP O60239 EXPRESSION TAG SEQADV 6IXG ALA A 260 UNP O60239 ARG 260 ENGINEERED MUTATION SEQADV 6IXG ALA A 261 UNP O60239 ARG 261 ENGINEERED MUTATION SEQADV 6IXG ALA A 262 UNP O60239 ARG 262 ENGINEERED MUTATION SEQADV 6IXG SER B 39 UNP O60239 EXPRESSION TAG SEQADV 6IXG HIS B 40 UNP O60239 EXPRESSION TAG SEQADV 6IXG ALA B 260 UNP O60239 ARG 260 ENGINEERED MUTATION SEQADV 6IXG ALA B 261 UNP O60239 ARG 261 ENGINEERED MUTATION SEQADV 6IXG ALA B 262 UNP O60239 ARG 262 ENGINEERED MUTATION SEQRES 1 A 228 SER HIS VAL ASP PRO ARG ILE GLN GLY GLU LEU GLU LYS SEQRES 2 A 228 LEU ASN GLN SER THR ASP ASP ILE ASN ARG ARG GLU THR SEQRES 3 A 228 GLU LEU GLU ASP ALA ARG GLN LYS PHE ARG SER VAL LEU SEQRES 4 A 228 VAL GLU ALA THR VAL LYS LEU ASP GLU LEU VAL LYS LYS SEQRES 5 A 228 ILE GLY LYS ALA VAL GLU ASP SER LYS PRO TYR TRP GLU SEQRES 6 A 228 ALA ARG ARG VAL ALA ARG GLN ALA GLN LEU GLU ALA GLN SEQRES 7 A 228 LYS ALA THR GLN ASP PHE GLN ARG ALA THR GLU VAL LEU SEQRES 8 A 228 ARG ALA ALA LYS GLU THR ILE SER LEU ALA GLU GLN ARG SEQRES 9 A 228 LEU LEU GLU ASP ASP LYS ARG GLN PHE ASP SER ALA TRP SEQRES 10 A 228 GLN GLU MET LEU ASN HIS ALA THR GLN ARG VAL MET GLU SEQRES 11 A 228 ALA GLU GLN THR LYS THR ARG SER GLU LEU VAL HIS LYS SEQRES 12 A 228 GLU THR ALA ALA ARG TYR ASN ALA ALA MET GLY ARG MET SEQRES 13 A 228 ARG GLN LEU GLU LYS LYS LEU LYS ARG ALA ILE ASN LYS SEQRES 14 A 228 SER LYS PRO TYR PHE GLU LEU LYS ALA LYS TYR TYR VAL SEQRES 15 A 228 GLN LEU GLU GLN LEU LYS LYS THR VAL ASP ASP LEU GLN SEQRES 16 A 228 ALA LYS LEU THR LEU ALA LYS GLY GLU TYR LYS MET ALA SEQRES 17 A 228 LEU LYS ASN LEU GLU MET ILE SER ASP GLU ILE HIS GLU SEQRES 18 A 228 ALA ALA ALA SER SER ALA MET SEQRES 1 B 228 SER HIS VAL ASP PRO ARG ILE GLN GLY GLU LEU GLU LYS SEQRES 2 B 228 LEU ASN GLN SER THR ASP ASP ILE ASN ARG ARG GLU THR SEQRES 3 B 228 GLU LEU GLU ASP ALA ARG GLN LYS PHE ARG SER VAL LEU SEQRES 4 B 228 VAL GLU ALA THR VAL LYS LEU ASP GLU LEU VAL LYS LYS SEQRES 5 B 228 ILE GLY LYS ALA VAL GLU ASP SER LYS PRO TYR TRP GLU SEQRES 6 B 228 ALA ARG ARG VAL ALA ARG GLN ALA GLN LEU GLU ALA GLN SEQRES 7 B 228 LYS ALA THR GLN ASP PHE GLN ARG ALA THR GLU VAL LEU SEQRES 8 B 228 ARG ALA ALA LYS GLU THR ILE SER LEU ALA GLU GLN ARG SEQRES 9 B 228 LEU LEU GLU ASP ASP LYS ARG GLN PHE ASP SER ALA TRP SEQRES 10 B 228 GLN GLU MET LEU ASN HIS ALA THR GLN ARG VAL MET GLU SEQRES 11 B 228 ALA GLU GLN THR LYS THR ARG SER GLU LEU VAL HIS LYS SEQRES 12 B 228 GLU THR ALA ALA ARG TYR ASN ALA ALA MET GLY ARG MET SEQRES 13 B 228 ARG GLN LEU GLU LYS LYS LEU LYS ARG ALA ILE ASN LYS SEQRES 14 B 228 SER LYS PRO TYR PHE GLU LEU LYS ALA LYS TYR TYR VAL SEQRES 15 B 228 GLN LEU GLU GLN LEU LYS LYS THR VAL ASP ASP LEU GLN SEQRES 16 B 228 ALA LYS LEU THR LEU ALA LYS GLY GLU TYR LYS MET ALA SEQRES 17 B 228 LEU LYS ASN LEU GLU MET ILE SER ASP GLU ILE HIS GLU SEQRES 18 B 228 ALA ALA ALA SER SER ALA MET HELIX 1 AA1 VAL A 41 ILE A 91 1 51 HELIX 2 AA2 GLY A 92 ASP A 146 1 55 HELIX 3 AA3 GLN A 150 LYS A 200 1 51 HELIX 4 AA4 LEU A 201 SER A 263 1 63 HELIX 5 AA5 ASP B 42 ILE B 91 1 50 HELIX 6 AA6 GLY B 92 ARG B 142 1 51 HELIX 7 AA7 PHE B 151 LEU B 201 1 51 HELIX 8 AA8 LEU B 201 ALA B 262 1 62 CRYST1 79.958 79.958 94.353 90.00 90.00 90.00 P 41 8 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 0.012507 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010598 0.00000