HEADER SIGNALING PROTEIN 10-DEC-18 6IXE TITLE CRYSTAL STRUCTURE OF SEMET APO SH3BP5 (I41) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH3 DOMAIN-BINDING PROTEIN 5; COMPND 3 CHAIN: A; 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 30-OCT-24 6IXE 1 REMARK REVDAT 2 27-MAR-19 6IXE 1 JRNL REVDAT 1 20-MAR-19 6IXE 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. 3.35 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) : 3.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.600 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 4689 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.271 REMARK 3 R VALUE (WORKING SET) : 0.269 REMARK 3 FREE R VALUE : 0.314 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 239 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 38.9011 - 4.2204 0.99 2288 122 0.2398 0.2853 REMARK 3 2 4.2204 - 3.3505 0.95 2162 117 0.3548 0.3859 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) : 0.650 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 42.510 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 1762 REMARK 3 ANGLE : 0.658 2357 REMARK 3 CHIRALITY : 0.019 262 REMARK 3 PLANARITY : 0.002 306 REMARK 3 DIHEDRAL : 11.417 702 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 6IXE 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_1300010107. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-18 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) : 0.9792 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 : 4777 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.350 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 (%) : 96.9 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15800 REMARK 200 FOR THE DATA SET : 30.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.41 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) : 0.35700 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SUCCINIC ACID (PH 7.0), 12% PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 39.62500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 39.62500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.03800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.62500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.01900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.62500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 81.05700 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.62500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.62500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 54.03800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 39.62500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 81.05700 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 39.62500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 27.01900 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 SER A 39 REMARK 465 HIS A 40 REMARK 465 LEU A 144 REMARK 465 GLU A 145 REMARK 465 ASP A 146 REMARK 465 ASP A 147 REMARK 465 LYS A 148 REMARK 465 ARG A 149 REMARK 465 GLN A 150 REMARK 465 ALA A 261 REMARK 465 ALA A 262 REMARK 465 SER A 263 REMARK 465 SER A 264 REMARK 465 ALA A 265 REMARK 465 MSE A 266 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 LYS A 90 -72.84 -62.65 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 SIN A 301 DBREF 6IXE A 41 266 UNP O60239 3BP5_HUMAN 41 266 SEQADV 6IXE SER A 39 UNP O60239 EXPRESSION TAG SEQADV 6IXE HIS A 40 UNP O60239 EXPRESSION TAG SEQADV 6IXE ALA A 167 UNP O60239 MET 167 ENGINEERED MUTATION SEQADV 6IXE ALA A 260 UNP O60239 ARG 260 ENGINEERED MUTATION SEQADV 6IXE ALA A 261 UNP O60239 ARG 261 ENGINEERED MUTATION SEQADV 6IXE ALA A 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 MSE LEU ASN HIS ALA THR GLN ARG VAL ALA 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 MSE GLY ARG MSE 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 MSE ALA SEQRES 17 A 228 LEU LYS ASN LEU GLU MSE ILE SER ASP GLU ILE HIS GLU SEQRES 18 A 228 ALA ALA ALA SER SER ALA MSE MODRES 6IXE MSE A 158 MET MODIFIED RESIDUE MODRES 6IXE MSE A 191 MET MODIFIED RESIDUE MODRES 6IXE MSE A 194 MET MODIFIED RESIDUE MODRES 6IXE MSE A 245 MET MODIFIED RESIDUE MODRES 6IXE MSE A 252 MET MODIFIED RESIDUE HET MSE A 158 8 HET MSE A 191 8 HET MSE A 194 8 HET MSE A 245 8 HET MSE A 252 8 HET SIN A 301 8 HETNAM MSE SELENOMETHIONINE HETNAM SIN SUCCINIC ACID FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 SIN C4 H6 O4 HELIX 1 AA1 VAL A 41 ILE A 91 1 51 HELIX 2 AA2 ILE A 91 LEU A 143 1 53 HELIX 3 AA3 ASP A 152 LYS A 200 1 49 HELIX 4 AA4 ALA A 204 ALA A 260 1 57 LINK C GLU A 157 N MSE A 158 1555 1555 1.33 LINK C MSE A 158 N LEU A 159 1555 1555 1.33 LINK C ALA A 190 N MSE A 191 1555 1555 1.33 LINK C MSE A 191 N GLY A 192 1555 1555 1.33 LINK C ARG A 193 N MSE A 194 1555 1555 1.33 LINK C MSE A 194 N ARG A 195 1555 1555 1.33 LINK C LYS A 244 N MSE A 245 1555 1555 1.33 LINK C MSE A 245 N ALA A 246 1555 1555 1.33 LINK C GLU A 251 N MSE A 252 1555 1555 1.33 LINK C MSE A 252 N ILE A 253 1555 1555 1.33 SITE 1 AC1 3 ASN A 53 GLN A 54 ASP A 57 CRYST1 79.250 79.250 108.076 90.00 90.00 90.00 I 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 0.012618 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009253 0.00000