HEADER STRUCTURAL PROTEIN 24-NOV-10 3PP5 TITLE HIGH-RESOLUTION STRUCTURE OF THE TRIMERIC SCAR/WAVE COMPLEX PRECURSOR TITLE 2 BRK1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BRK1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN BRICK1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_COMMON: SLIME MOLD; SOURCE 4 ORGANISM_TAXID: 44689; SOURCE 5 GENE: BRK1, DDB_G0279175, HSPC300; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P1 KEYWDS TRIPLE COILED-COIL, PRECURSOR OF THE SCAR-WAVE COMPLEX, ABI, SCAR, KEYWDS 2 STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LINKNER,G.WITTE,U.CURTH,J.FAIX REVDAT 5 21-FEB-24 3PP5 1 REMARK SEQADV REVDAT 4 08-NOV-17 3PP5 1 REMARK REVDAT 3 28-MAR-12 3PP5 1 JRNL VERSN REVDAT 2 06-JUL-11 3PP5 1 REVDAT 1 08-JUN-11 3PP5 0 JRNL AUTH J.LINKNER,G.WITTE,T.STRADAL,U.CURTH,J.FAIX JRNL TITL HIGH-RESOLUTION X-RAY STRUCTURE OF THE TRIMERIC JRNL TITL 2 SCAR/WAVE-COMPLEX PRECURSOR BRK1. JRNL REF PLOS ONE V. 6 21327 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 21701600 JRNL DOI 10.1371/JOURNAL.PONE.0021327 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 16144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 806 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 19.3906 - 2.7237 0.97 2550 134 0.1663 0.1805 REMARK 3 2 2.7237 - 2.1628 0.99 2582 136 0.1461 0.1694 REMARK 3 3 2.1628 - 1.8897 0.99 2568 135 0.1424 0.1941 REMARK 3 4 1.8897 - 1.7170 0.99 2575 135 0.1618 0.1838 REMARK 3 5 1.7170 - 1.5940 0.99 2559 135 0.1510 0.1746 REMARK 3 6 1.5940 - 1.5001 0.98 2504 131 0.1567 0.1673 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 : 0.38 REMARK 3 B_SOL : 64.61 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.43880 REMARK 3 B22 (A**2) : 2.43880 REMARK 3 B33 (A**2) : -4.87770 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 : 0.013 621 REMARK 3 ANGLE : 1.245 843 REMARK 3 CHIRALITY : 0.074 94 REMARK 3 PLANARITY : 0.005 108 REMARK 3 DIHEDRAL : 15.787 248 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): 18.0149 -6.0166 17.0839 REMARK 3 T TENSOR REMARK 3 T11: 0.0800 T22: 0.0661 REMARK 3 T33: 0.0801 T12: -0.0017 REMARK 3 T13: -0.0031 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: -0.0514 L22: 0.2143 REMARK 3 L33: 0.3073 L12: -0.0002 REMARK 3 L13: -0.2194 L23: 0.4286 REMARK 3 S TENSOR REMARK 3 S11: 0.0010 S12: 0.0128 S13: 0.0184 REMARK 3 S21: 0.0140 S22: 0.0410 S23: -0.0281 REMARK 3 S31: -0.0625 S32: -0.0246 S33: 0.0073 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 3PP5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062647. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-09; 10-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SLS; ESRF REMARK 200 BEAMLINE : X06DA; ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0722; 0.8726 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR (SI 111); REMARK 200 SILICON 111 CRYSTAL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD; MARMOSAIC REMARK 200 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16181 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 12.09 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.950 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD, MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX (ANOMALOUS DATASET) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% (V/V) MPD, 0.2 M CACL2, PH 7.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 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 59.09500 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 59.09500 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 59.09500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -179.0 KCAL/MOL 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 BIOMT1 2 -0.500000 -0.866025 0.000000 19.57000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -33.89623 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 39.14000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 VAL A 66 REMARK 465 GLN A 67 REMARK 465 GLU A 68 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASN A 46 O HOH A 110 2.06 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 69 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 70 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 71 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 72 DBREF 3PP5 A 1 68 UNP Q54X65 BRK1_DICDI 1 68 SEQADV 3PP5 GLY A -4 UNP Q54X65 EXPRESSION TAG SEQADV 3PP5 PRO A -3 UNP Q54X65 EXPRESSION TAG SEQADV 3PP5 LEU A -2 UNP Q54X65 EXPRESSION TAG SEQADV 3PP5 GLY A -1 UNP Q54X65 EXPRESSION TAG SEQADV 3PP5 SER A 0 UNP Q54X65 EXPRESSION TAG SEQRES 1 A 73 GLY PRO LEU GLY SER MET SER THR LYS THR ASN ILE GLN SEQRES 2 A 73 LYS ASP TRP GLU GLN ARG GLU PHE ILE GLU ASP MET SER SEQRES 3 A 73 ILE ASN ILE GLN LYS ILE VAL GLU PHE LEU ASN LYS PHE SEQRES 4 A 73 GLU LEU SER THR ARG ASN LYS LEU SER ASP LEU ASN GLU SEQRES 5 A 73 LYS LEU THR ILE LEU ASP ARG GLN VAL ASP TYR LEU GLU SEQRES 6 A 73 ALA THR PHE LYS THR VAL GLN GLU HET MPD A 69 8 HET MRD A 70 8 HET CA A 71 1 HET CA A 72 1 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM CA CALCIUM ION FORMUL 2 MPD C6 H14 O2 FORMUL 3 MRD C6 H14 O2 FORMUL 4 CA 2(CA 2+) FORMUL 6 HOH *107(H2 O) HELIX 1 1 THR A 5 THR A 65 1 61 SITE 1 AC1 5 TRP A 11 LYS A 48 ASP A 53 HOH A 79 SITE 2 AC1 5 HOH A 126 SITE 1 AC2 3 PHE A 30 ASN A 32 HOH A 106 SITE 1 AC3 6 GLU A 15 GLU A 18 ASP A 57 HOH A 87 SITE 2 AC3 6 HOH A 98 HOH A 114 SITE 1 AC4 6 GLU A 15 GLU A 18 ASP A 57 GLU A 60 SITE 2 AC4 6 HOH A 84 HOH A 86 CRYST1 39.140 39.140 118.190 90.00 90.00 120.00 P 63 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 0.025549 0.014751 0.000000 0.00000 SCALE2 0.000000 0.029502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008461 0.00000