HEADER ACTIN-BINDING PROTEIN 26-JUN-97 1YPR TITLE SACCHAROMYCES CEREVISIAE (YEAST) PROFILIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROFILIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACTIN-BINDING PROTEIN, PROFILIN, CYTOSKELETON EXPDTA X-RAY DIFFRACTION AUTHOR J.C.EADS,N.M.MAHONEY,S.C.ALMO REVDAT 5 03-APR-24 1YPR 1 REMARK REVDAT 4 14-FEB-24 1YPR 1 REMARK REVDAT 3 24-FEB-09 1YPR 1 VERSN REVDAT 2 01-APR-03 1YPR 1 JRNL REVDAT 1 31-DEC-97 1YPR 0 JRNL AUTH J.C.EADS,N.M.MAHONEY,S.VOROBIEV,B.K.HAARER,S.C.ALMO JRNL TITL STRUCTURE DETERMINATION AND CHARACTERIZATION OF JRNL TITL 2 SACCHAROMYCES CEREVISIAE PROFILIN JRNL REF BIOCHEMISTRY V. 37 11171 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9698363 JRNL DOI 10.1021/BI9720033 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 11875 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 620 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1100 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 67 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1912 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 39 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.20 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.468 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.300 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : RESTRAINTS, IN EARLY STAGES OF REFINEMENT REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YPR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177424. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12068 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 10.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.21700 REMARK 200 R SYM FOR SHELL (I) : 0.21300 REMARK 200 FOR SHELL : 2.750 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: ACANTHAMOEBA PROFILIN P1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M LI SULFATE, 0.1 M TRIS, PH 8.5, REMARK 280 0.01M NICL2 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 100.86667 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 50.43333 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 75.65000 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 25.21667 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 126.08333 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 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 ASP A 82 -123.50 63.93 REMARK 500 THR A 91 -160.61 -109.24 REMARK 500 ALA B 30 147.90 -170.71 REMARK 500 ALA B 53 -60.73 -24.53 REMARK 500 GLN B 63 48.09 36.12 REMARK 500 ALA B 72 96.08 -165.81 REMARK 500 ASP B 73 -166.94 -120.24 REMARK 500 ASP B 82 -112.51 70.53 REMARK 500 THR B 91 -163.65 -103.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 119 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1YPR A 1 125 UNP P07274 PROF_YEAST 2 126 DBREF 1YPR B 1 125 UNP P07274 PROF_YEAST 2 126 SEQRES 1 A 125 SER TRP GLN ALA TYR THR ASP ASN LEU ILE GLY THR GLY SEQRES 2 A 125 LYS VAL ASP LYS ALA VAL ILE TYR SER ARG ALA GLY ASP SEQRES 3 A 125 ALA VAL TRP ALA THR SER GLY GLY LEU SER LEU GLN PRO SEQRES 4 A 125 ASN GLU ILE GLY GLU ILE VAL GLN GLY PHE ASP ASN PRO SEQRES 5 A 125 ALA GLY LEU GLN SER ASN GLY LEU HIS ILE GLN GLY GLN SEQRES 6 A 125 LYS PHE MET LEU LEU ARG ALA ASP ASP ARG SER ILE TYR SEQRES 7 A 125 GLY ARG HIS ASP ALA GLU GLY VAL VAL CYS VAL ARG THR SEQRES 8 A 125 LYS GLN THR VAL ILE ILE ALA HIS TYR PRO PRO THR VAL SEQRES 9 A 125 GLN ALA GLY GLU ALA THR LYS ILE VAL GLU GLN LEU ALA SEQRES 10 A 125 ASP TYR LEU ILE GLY VAL GLN TYR SEQRES 1 B 125 SER TRP GLN ALA TYR THR ASP ASN LEU ILE GLY THR GLY SEQRES 2 B 125 LYS VAL ASP LYS ALA VAL ILE TYR SER ARG ALA GLY ASP SEQRES 3 B 125 ALA VAL TRP ALA THR SER GLY GLY LEU SER LEU GLN PRO SEQRES 4 B 125 ASN GLU ILE GLY GLU ILE VAL GLN GLY PHE ASP ASN PRO SEQRES 5 B 125 ALA GLY LEU GLN SER ASN GLY LEU HIS ILE GLN GLY GLN SEQRES 6 B 125 LYS PHE MET LEU LEU ARG ALA ASP ASP ARG SER ILE TYR SEQRES 7 B 125 GLY ARG HIS ASP ALA GLU GLY VAL VAL CYS VAL ARG THR SEQRES 8 B 125 LYS GLN THR VAL ILE ILE ALA HIS TYR PRO PRO THR VAL SEQRES 9 B 125 GLN ALA GLY GLU ALA THR LYS ILE VAL GLU GLN LEU ALA SEQRES 10 B 125 ASP TYR LEU ILE GLY VAL GLN TYR FORMUL 3 HOH *39(H2 O) HELIX 1 1 TRP A 2 THR A 12 1 11 HELIX 2 2 PRO A 39 PHE A 49 1 11 HELIX 3 3 ALA A 53 ASN A 58 1 6 HELIX 4 4 ALA A 106 VAL A 123 1 18 HELIX 5 5 GLN B 3 THR B 12 1 10 HELIX 6 6 PRO B 39 PHE B 49 1 11 HELIX 7 7 PRO B 52 ASN B 58 5 7 HELIX 8 8 ALA B 106 VAL B 123 1 18 SHEET 1 A 6 MET A 68 ALA A 72 0 SHEET 2 A 6 SER A 76 HIS A 81 -1 N ARG A 80 O MET A 68 SHEET 3 A 6 GLU A 84 ARG A 90 -1 N CYS A 88 O ILE A 77 SHEET 4 A 6 THR A 94 TYR A 100 -1 N TYR A 100 O GLY A 85 SHEET 5 A 6 LYS A 17 SER A 22 -1 N TYR A 21 O VAL A 95 SHEET 6 A 6 VAL A 28 SER A 32 -1 N SER A 32 O ALA A 18 SHEET 1 B 2 LEU A 60 ILE A 62 0 SHEET 2 B 2 GLN A 65 PHE A 67 -1 N PHE A 67 O LEU A 60 SHEET 1 C 6 MET B 68 ALA B 72 0 SHEET 2 C 6 SER B 76 HIS B 81 -1 N ARG B 80 O MET B 68 SHEET 3 C 6 GLU B 84 ARG B 90 -1 N CYS B 88 O ILE B 77 SHEET 4 C 6 THR B 94 TYR B 100 -1 N TYR B 100 O GLY B 85 SHEET 5 C 6 LYS B 17 SER B 22 -1 N TYR B 21 O VAL B 95 SHEET 6 C 6 VAL B 28 SER B 32 -1 N SER B 32 O ALA B 18 SHEET 1 D 2 LEU B 60 ILE B 62 0 SHEET 2 D 2 GLN B 65 PHE B 67 -1 N PHE B 67 O LEU B 60 CRYST1 58.100 58.100 151.300 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 0.017212 0.009937 0.000000 0.00000 SCALE2 0.000000 0.019874 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006609 0.00000 MTRIX1 1 0.427531 0.806755 -0.407876 16.92810 1 MTRIX2 1 -0.624338 0.589808 0.512180 -18.73800 1 MTRIX3 1 0.653773 0.035680 0.755849 -32.37120 1