HEADER TRANSPORT PROTEIN 22-AUG-14 4W7Y TITLE DIMERIC BAP29 VDED WITH DISULFIDE BONDS IN CRYSTAL CONTACTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-CELL RECEPTOR-ASSOCIATED PROTEIN 29; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 168-229; COMPND 5 SYNONYM: BAP29; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BCAP29, BAP29; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COILED COIL, NANOMATERIAL, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.M.QUISTGAARD REVDAT 2 19-NOV-14 4W7Y 1 JRNL REVDAT 1 29-OCT-14 4W7Y 0 JRNL AUTH E.M.QUISTGAARD JRNL TITL A DISULFIDE POLYMERIZED PROTEIN CRYSTAL. JRNL REF CHEM.COMMUN.(CAMB.) V. 50 14995 2014 JRNL REFN ESSN 1364-548X JRNL PMID 25327138 JRNL DOI 10.1039/C4CC07326F REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16718 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 787 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 34.3180 - 4.5402 1.00 2639 143 0.1831 0.2049 REMARK 3 2 4.5402 - 3.6049 1.00 2667 132 0.1702 0.2229 REMARK 3 3 3.6049 - 3.1496 1.00 2667 121 0.2057 0.2707 REMARK 3 4 3.1496 - 2.8618 1.00 2648 139 0.2200 0.2605 REMARK 3 5 2.8618 - 2.6567 1.00 2659 143 0.2311 0.2964 REMARK 3 6 2.6567 - 2.5002 1.00 2651 109 0.2550 0.2701 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.950 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 : 0.012 1065 REMARK 3 ANGLE : 1.275 1411 REMARK 3 CHIRALITY : 0.053 158 REMARK 3 PLANARITY : 0.006 183 REMARK 3 DIHEDRAL : 17.189 440 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' OR CHAIN 'B' REMARK 3 ORIGIN FOR THE GROUP (A): 71.3112 -8.0539 3.9062 REMARK 3 T TENSOR REMARK 3 T11: 0.7042 T22: 0.3975 REMARK 3 T33: 0.5048 T12: 0.1281 REMARK 3 T13: -0.0007 T23: 0.0776 REMARK 3 L TENSOR REMARK 3 L11: 1.2608 L22: 5.6933 REMARK 3 L33: 0.4455 L12: -1.9849 REMARK 3 L13: 0.4097 L23: -0.9965 REMARK 3 S TENSOR REMARK 3 S11: 0.0137 S12: -0.1544 S13: -0.3698 REMARK 3 S21: -0.4709 S22: 0.0961 S23: -0.1191 REMARK 3 S31: 0.4826 S32: 0.1735 S33: -0.1445 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 4W7Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000203351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16720 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 34.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 17.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.930 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: GROWN IN 34% 2-METHYL-2,4-PENTANEDIOL REMARK 280 (MPD), 100 MM NA ACETATE PH 4.6 AND 20 MM CACL2 USING SEMET REMARK 280 LABELED PROTEIN PURIFIED IN 20 MM TRIS PH 8, 150 MM NACL AND 2 REMARK 280 MM TRIS(2-CARBOXYETHYL)PHOSPHINE (TECEP) AND CONCENTRATED TO ~13 REMARK 280 MG/ML. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 20.42000 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 10.21000 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 15.31500 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 5.10500 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 25.52500 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: 3650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER B 227 GLU B 228 143.68 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 MPD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 302 DBREF 4W7Y A 168 229 UNP Q9UHQ4 BAP29_HUMAN 168 229 DBREF 4W7Y B 168 229 UNP Q9UHQ4 BAP29_HUMAN 168 229 SEQADV 4W7Y SER A 166 UNP Q9UHQ4 EXPRESSION TAG SEQADV 4W7Y MSE A 167 UNP Q9UHQ4 EXPRESSION TAG SEQADV 4W7Y SER B 166 UNP Q9UHQ4 EXPRESSION TAG SEQADV 4W7Y MSE B 167 UNP Q9UHQ4 EXPRESSION TAG SEQRES 1 A 64 SER MSE ASP GLU GLU CYS VAL LEU GLU ALA GLU ASN LYS SEQRES 2 A 64 LYS LEU VAL GLU ASP GLN GLU LYS LEU LYS THR GLU LEU SEQRES 3 A 64 ARG LYS THR SER ASP ALA LEU SER LYS ALA GLN ASN ASP SEQRES 4 A 64 VAL MSE GLU MSE LYS MSE GLN SER GLU ARG LEU SER LYS SEQRES 5 A 64 GLU TYR ASP GLN LEU LEU LYS GLU HIS SER GLU LEU SEQRES 1 B 64 SER MSE ASP GLU GLU CYS VAL LEU GLU ALA GLU ASN LYS SEQRES 2 B 64 LYS LEU VAL GLU ASP GLN GLU LYS LEU LYS THR GLU LEU SEQRES 3 B 64 ARG LYS THR SER ASP ALA LEU SER LYS ALA GLN ASN ASP SEQRES 4 B 64 VAL MSE GLU MSE LYS MSE GLN SER GLU ARG LEU SER LYS SEQRES 5 B 64 GLU TYR ASP GLN LEU LEU LYS GLU HIS SER GLU LEU MODRES 4W7Y MSE A 206 MET MODIFIED RESIDUE MODRES 4W7Y MSE A 208 MET MODIFIED RESIDUE MODRES 4W7Y MSE A 210 MET MODIFIED RESIDUE MODRES 4W7Y MSE B 206 MET MODIFIED RESIDUE MODRES 4W7Y MSE B 208 MET MODIFIED RESIDUE MODRES 4W7Y MSE B 210 MET MODIFIED RESIDUE HET MSE A 167 8 HET MSE A 206 8 HET MSE A 208 8 HET MSE A 210 8 HET MSE B 167 8 HET MSE B 206 8 HET MSE B 208 8 HET MSE B 210 8 HET MPD A 301 8 HET MPD B 301 8 HET ACT B 302 4 HETNAM MSE SELENOMETHIONINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM ACT ACETATE ION FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 MPD 2(C6 H14 O2) FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 HOH *31(H2 O) HELIX 1 AA1 SER A 166 HIS A 226 1 61 HELIX 2 AA2 MSE B 167 SER B 227 1 61 SSBOND 1 CYS A 171 CYS B 171 1555 3665 2.07 LINK C SER A 166 N MSE A 167 1555 1555 1.32 LINK C MSE A 167 N ASP A 168 1555 1555 1.33 LINK C VAL A 205 N MSE A 206 1555 1555 1.32 LINK C MSE A 206 N GLU A 207 1555 1555 1.33 LINK C GLU A 207 N MSE A 208 1555 1555 1.32 LINK C MSE A 208 N LYS A 209 1555 1555 1.33 LINK C LYS A 209 N MSE A 210 1555 1555 1.33 LINK C MSE A 210 N GLN A 211 1555 1555 1.33 LINK C SER B 166 N MSE B 167 1555 1555 1.33 LINK C MSE B 167 N ASP B 168 1555 1555 1.33 LINK C VAL B 205 N MSE B 206 1555 1555 1.33 LINK C MSE B 206 N GLU B 207 1555 1555 1.33 LINK C GLU B 207 N MSE B 208 1555 1555 1.33 LINK C MSE B 208 N LYS B 209 1555 1555 1.33 LINK C LYS B 209 N MSE B 210 1555 1555 1.33 LINK C MSE B 210 N GLN B 211 1555 1555 1.33 SITE 1 AC1 6 GLU A 190 THR A 194 GLU B 225 HIS B 226 SITE 2 AC1 6 GLU B 228 HOH B 402 SITE 1 AC2 3 LYS A 188 ASP B 183 LYS B 186 SITE 1 AC3 4 CYS A 171 GLU A 174 LYS A 178 ASP B 168 CRYST1 118.870 118.870 30.630 90.00 90.00 120.00 P 65 12 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 0.008413 0.004857 0.000000 0.00000 SCALE2 0.000000 0.009714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032648 0.00000