HEADER PROTEIN BINDING 30-AUG-10 3ONX TITLE CRYSTAL STRUCTURE OF A DOMAIN OF A PROTEIN INVOLVED IN FORMATION OF TITLE 2 ACTIN CYTOSKELETON COMPND MOL_ID: 1; COMPND 2 MOLECULE: BUD SITE SELECTION PROTEIN 6; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: COILED-COIL DOMAIN (UNP RESIDUES 549-688); COMPND 5 SYNONYM: ACTIN-INTERACTING PROTEIN 3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: AIP3, BUD6, L8543.5, YLR319C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS COILED-COIL, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.TU,M.J.ECK REVDAT 4 06-NOV-24 3ONX 1 SEQADV LINK REVDAT 3 26-DEC-12 3ONX 1 JRNL REVDAT 2 05-DEC-12 3ONX 1 JRNL REVDAT 1 12-OCT-11 3ONX 0 JRNL AUTH D.TU,B.R.GRAZIANO,E.PARK,W.ZHENG,Y.LI,B.L.GOODE,M.J.ECK JRNL TITL STRUCTURE OF THE FORMIN-INTERACTION DOMAIN OF THE ACTIN JRNL TITL 2 NUCLEATION-PROMOTING FACTOR BUD6. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 E3424 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 23161908 JRNL DOI 10.1073/PNAS.1203035109 REMARK 2 REMARK 2 RESOLUTION. 2.90 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.700 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 17076 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1710 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 35.0309 - 6.6339 0.99 1339 135 0.1768 0.1659 REMARK 3 2 6.6339 - 5.2713 1.00 1365 128 0.2641 0.2802 REMARK 3 3 5.2713 - 4.6067 0.98 1347 149 0.2020 0.2391 REMARK 3 4 4.6067 - 4.1862 1.00 1350 136 0.1902 0.2843 REMARK 3 5 4.1862 - 3.8866 0.99 1349 152 0.1956 0.2580 REMARK 3 6 3.8866 - 3.6577 1.00 1360 135 0.2080 0.2861 REMARK 3 7 3.6577 - 3.4747 1.00 1321 169 0.2422 0.2764 REMARK 3 8 3.4747 - 3.3235 0.99 1324 150 0.2850 0.3360 REMARK 3 9 3.3235 - 3.1957 0.98 1341 146 0.3169 0.3804 REMARK 3 10 3.1957 - 3.0855 0.92 1192 155 0.3436 0.3709 REMARK 3 11 3.0855 - 2.9891 0.86 1196 136 0.3486 0.4292 REMARK 3 12 2.9891 - 2.9037 0.66 882 119 0.3522 0.3773 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 : 0.32 REMARK 3 B_SOL : 65.01 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.880 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) : 6.23930 REMARK 3 B22 (A**2) : 9.29550 REMARK 3 B33 (A**2) : -15.53490 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 24.97080 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 : 0.010 2066 REMARK 3 ANGLE : 1.189 2772 REMARK 3 CHIRALITY : 0.072 320 REMARK 3 PLANARITY : 0.004 356 REMARK 3 DIHEDRAL : 22.092 820 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 3ONX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000061353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : MD2 MICRODIFFRACTOMETER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17136 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9% PEG 3350, 85 MM SODIUM MALONATE (PH REMARK 280 7.0), 25% GLYCEROL, 10 MM DTT, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 33.71200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 5230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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 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 548 REMARK 465 SER A 549 REMARK 465 ALA A 550 REMARK 465 LYS A 551 REMARK 465 ASN A 552 REMARK 465 SER A 553 REMARK 465 SER A 554 REMARK 465 GLN A 680 REMARK 465 GLU A 681 REMARK 465 LYS A 682 REMARK 465 ASN A 683 REMARK 465 PRO A 684 REMARK 465 SER A 685 REMARK 465 ARG A 686 REMARK 465 SER A 687 REMARK 465 LYS A 688 REMARK 465 GLY B 548 REMARK 465 SER B 549 REMARK 465 ALA B 550 REMARK 465 LYS B 551 REMARK 465 ASN B 552 REMARK 465 SER B 553 REMARK 465 SER B 554 REMARK 465 GLN B 680 REMARK 465 GLU B 681 REMARK 465 LYS B 682 REMARK 465 ASN B 683 REMARK 465 PRO B 684 REMARK 465 SER B 685 REMARK 465 ARG B 686 REMARK 465 SER B 687 REMARK 465 LYS B 688 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 LEU A 603 -8.04 -54.56 REMARK 500 ILE A 656 -2.43 -58.75 REMARK 500 GLU B 593 -72.29 -122.53 REMARK 500 ARG B 595 -9.77 79.72 REMARK 500 ALA B 599 161.04 -48.80 REMARK 500 PRO B 629 -71.01 -45.11 REMARK 500 GLU B 678 -32.07 -136.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OKQ RELATED DB: PDB DBREF 3ONX A 549 688 UNP P41697 BUD6_YEAST 549 688 DBREF 3ONX B 549 688 UNP P41697 BUD6_YEAST 549 688 SEQADV 3ONX GLY A 548 UNP P41697 EXPRESSION TAG SEQADV 3ONX GLY B 548 UNP P41697 EXPRESSION TAG SEQRES 1 A 141 GLY SER ALA LYS ASN SER SER ASN ARG MSE TYR MSE GLU SEQRES 2 A 141 LYS SER GLN THR GLU LEU GLY ASP LEU SER ASP THR LEU SEQRES 3 A 141 LEU SER LYS VAL ASP ASP LEU GLN ASP VAL ILE GLU ILE SEQRES 4 A 141 MSE ARG LYS ASP VAL ALA GLU ARG ARG SER GLN PRO ALA SEQRES 5 A 141 LYS LYS LYS LEU GLU THR VAL SER LYS ASP LEU GLU ASN SEQRES 6 A 141 ALA GLN ALA ASP VAL LEU LYS LEU GLN GLU PHE ILE ASP SEQRES 7 A 141 THR GLU LYS PRO HIS TRP LYS LYS THR TRP GLU ALA GLU SEQRES 8 A 141 LEU ASP LYS VAL CYS GLU GLU GLN GLN PHE LEU THR LEU SEQRES 9 A 141 GLN GLU GLU LEU ILE LEU ASP LEU LYS GLU ASP LEU GLY SEQRES 10 A 141 LYS ALA LEU GLU THR PHE ASP LEU ILE LYS LEU CYS CYS SEQRES 11 A 141 GLU GLU GLN GLU LYS ASN PRO SER ARG SER LYS SEQRES 1 B 141 GLY SER ALA LYS ASN SER SER ASN ARG MSE TYR MSE GLU SEQRES 2 B 141 LYS SER GLN THR GLU LEU GLY ASP LEU SER ASP THR LEU SEQRES 3 B 141 LEU SER LYS VAL ASP ASP LEU GLN ASP VAL ILE GLU ILE SEQRES 4 B 141 MSE ARG LYS ASP VAL ALA GLU ARG ARG SER GLN PRO ALA SEQRES 5 B 141 LYS LYS LYS LEU GLU THR VAL SER LYS ASP LEU GLU ASN SEQRES 6 B 141 ALA GLN ALA ASP VAL LEU LYS LEU GLN GLU PHE ILE ASP SEQRES 7 B 141 THR GLU LYS PRO HIS TRP LYS LYS THR TRP GLU ALA GLU SEQRES 8 B 141 LEU ASP LYS VAL CYS GLU GLU GLN GLN PHE LEU THR LEU SEQRES 9 B 141 GLN GLU GLU LEU ILE LEU ASP LEU LYS GLU ASP LEU GLY SEQRES 10 B 141 LYS ALA LEU GLU THR PHE ASP LEU ILE LYS LEU CYS CYS SEQRES 11 B 141 GLU GLU GLN GLU LYS ASN PRO SER ARG SER LYS MODRES 3ONX MSE A 557 MET SELENOMETHIONINE MODRES 3ONX MSE A 559 MET SELENOMETHIONINE MODRES 3ONX MSE A 587 MET SELENOMETHIONINE MODRES 3ONX MSE B 557 MET SELENOMETHIONINE MODRES 3ONX MSE B 559 MET SELENOMETHIONINE MODRES 3ONX MSE B 587 MET SELENOMETHIONINE HET MSE A 557 8 HET MSE A 559 8 HET MSE A 587 8 HET MSE B 557 8 HET MSE B 559 8 HET MSE B 587 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 6(C5 H11 N O2 SE) HELIX 1 1 ASN A 555 ARG A 595 1 41 HELIX 2 2 LYS A 601 GLU A 678 1 78 HELIX 3 3 ASN B 555 GLU B 593 1 39 HELIX 4 4 ALA B 599 CYS B 677 1 79 LINK C ARG A 556 N MSE A 557 1555 1555 1.32 LINK C MSE A 557 N TYR A 558 1555 1555 1.34 LINK C TYR A 558 N MSE A 559 1555 1555 1.32 LINK C MSE A 559 N GLU A 560 1555 1555 1.33 LINK C ILE A 586 N MSE A 587 1555 1555 1.32 LINK C MSE A 587 N ARG A 588 1555 1555 1.33 LINK C ARG B 556 N MSE B 557 1555 1555 1.33 LINK C MSE B 557 N TYR B 558 1555 1555 1.33 LINK C TYR B 558 N MSE B 559 1555 1555 1.33 LINK C MSE B 559 N GLU B 560 1555 1555 1.33 LINK C ILE B 586 N MSE B 587 1555 1555 1.33 LINK C MSE B 587 N ARG B 588 1555 1555 1.33 CRYST1 53.307 67.424 58.755 90.00 94.51 90.00 P 1 21 1 4 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 0.018759 0.000000 0.001480 0.00000 SCALE2 0.000000 0.014832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017073 0.00000