HEADER STRUCTURAL REGULATION PROTEIN 13-APR-99 1CJF TITLE PROFILIN BINDS PROLINE-RICH LIGANDS IN TWO DISTINCT AMIDE BACKBONE TITLE 2 ORIENTATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (HUMAN PLATELET PROFILIN); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HMC FLUOROPHORE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTEIN (PROLINE PEPTIDE); COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: BL21(DE3); SOURCE 6 CELLULAR_LOCATION: CYTOPLASM; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES KEYWDS PROFILIN, ACTIN-BINDING PROTEIN, CYTOSKELETON, POLY-L-PROLINE, KEYWDS 2 STRUCTURAL REGULATION PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.M.MAHONEY,A.A.FEDOROV,E.FEDOROV,D.A.ROZWARSKI,S.C.ALMO REVDAT 3 09-AUG-23 1CJF 1 REMARK LINK REVDAT 2 24-FEB-09 1CJF 1 VERSN REVDAT 1 07-JUL-99 1CJF 0 JRNL AUTH N.M.MAHONEY,D.A.ROZWARSKI,E.FEDOROV,A.A.FEDOROV,S.C.ALMO JRNL TITL PROFILIN BINDS PROLINE-RICH LIGANDS IN TWO DISTINCT AMIDE JRNL TITL 2 BACKBONE ORIENTATIONS. JRNL REF NAT.STRUCT.BIOL. V. 6 666 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10404225 JRNL DOI 10.1038/10722 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 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) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 11957 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) : 0.195 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 2287 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.15 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) : 0.26 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) : 0.38 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) : 1.390 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.07 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.729 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 : NULL 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 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CJF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-99. REMARK 100 THE DEPOSITION ID IS D_1000000844. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS X1000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11957 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 1FIL 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): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M AMMONIUM SULFATE, 0.1 M HEPES PH REMARK 280 7.5, 0.1 M NACL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 52.70000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.70000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.90000 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, D 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 ALA A 1 REMARK 465 ALA B 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO D 16 CA C O CB CG CD 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 26 -82.54 71.43 REMARK 500 PRO A 28 144.32 -39.33 REMARK 500 LYS A 37 -148.21 -97.95 REMARK 500 ASP A 80 153.68 -48.55 REMARK 500 GLU A 82 -62.24 -121.29 REMARK 500 SER A 91 117.62 -39.61 REMARK 500 ASP B 26 -66.90 68.49 REMARK 500 PRO B 28 130.79 -37.03 REMARK 500 LYS B 37 -148.71 -108.58 REMARK 500 GLU B 82 -63.35 -103.89 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 HOM C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HOM D 1 DBREF 1CJF A 1 139 UNP P07737 PROF1_HUMAN 1 139 DBREF 1CJF B 1 139 UNP P07737 PROF1_HUMAN 1 139 DBREF 1CJF C 2 16 PDB 1CJF 1CJF 2 16 DBREF 1CJF D 2 16 PDB 1CJF 1CJF 2 16 SEQRES 1 A 139 ALA GLY TRP ASN ALA TYR ILE ASP ASN LEU MET ALA ASP SEQRES 2 A 139 GLY THR CYS GLN ASP ALA ALA ILE VAL GLY TYR LYS ASP SEQRES 3 A 139 SER PRO SER VAL TRP ALA ALA VAL PRO GLY LYS THR PHE SEQRES 4 A 139 VAL ASN ILE THR PRO ALA GLU VAL GLY VAL LEU VAL GLY SEQRES 5 A 139 LYS ASP ARG SER SER PHE TYR VAL ASN GLY LEU THR LEU SEQRES 6 A 139 GLY GLY GLN LYS CYS SER VAL ILE ARG ASP SER LEU LEU SEQRES 7 A 139 GLN ASP GLY GLU PHE SER MET ASP LEU ARG THR LYS SER SEQRES 8 A 139 THR GLY GLY ALA PRO THR PHE ASN VAL THR VAL THR LYS SEQRES 9 A 139 THR ASP LYS THR LEU VAL LEU LEU MET GLY LYS GLU GLY SEQRES 10 A 139 VAL HIS GLY GLY LEU ILE ASN LYS LYS CYS TYR GLU MET SEQRES 11 A 139 ALA SER HIS LEU ARG ARG SER GLN TYR SEQRES 1 C 15 PRO PRO PRO PRO PRO PRO PRO PRO PRO PRO PRO PRO PRO SEQRES 2 C 15 PRO PRO SEQRES 1 B 139 ALA GLY TRP ASN ALA TYR ILE ASP ASN LEU MET ALA ASP SEQRES 2 B 139 GLY THR CYS GLN ASP ALA ALA ILE VAL GLY TYR LYS ASP SEQRES 3 B 139 SER PRO SER VAL TRP ALA ALA VAL PRO GLY LYS THR PHE SEQRES 4 B 139 VAL ASN ILE THR PRO ALA GLU VAL GLY VAL LEU VAL GLY SEQRES 5 B 139 LYS ASP ARG SER SER PHE TYR VAL ASN GLY LEU THR LEU SEQRES 6 B 139 GLY GLY GLN LYS CYS SER VAL ILE ARG ASP SER LEU LEU SEQRES 7 B 139 GLN ASP GLY GLU PHE SER MET ASP LEU ARG THR LYS SER SEQRES 8 B 139 THR GLY GLY ALA PRO THR PHE ASN VAL THR VAL THR LYS SEQRES 9 B 139 THR ASP LYS THR LEU VAL LEU LEU MET GLY LYS GLU GLY SEQRES 10 B 139 VAL HIS GLY GLY LEU ILE ASN LYS LYS CYS TYR GLU MET SEQRES 11 B 139 ALA SER HIS LEU ARG ARG SER GLN TYR SEQRES 1 D 15 PRO PRO PRO PRO PRO PRO PRO PRO PRO PRO PRO PRO PRO SEQRES 2 D 15 PRO PRO HET HOM C 1 16 HET HOM D 1 16 HETNAM HOM 7-HYDROXY-4-METHYL-3-(2-HYDROXY-ETHYL)COUMARIN FORMUL 5 HOM 2(C12 H12 O4) FORMUL 7 HOH *24(H2 O) HELIX 1 1 TRP A 3 MET A 11 5 9 HELIX 2 2 PHE A 39 ASN A 41 5 3 HELIX 3 3 PRO A 44 VAL A 51 1 8 HELIX 4 4 PHE A 58 ASN A 61 1 4 HELIX 5 5 GLY A 120 SER A 137 1 18 HELIX 6 6 TRP B 3 MET B 11 5 9 HELIX 7 7 PHE B 39 ASN B 41 5 3 HELIX 8 8 PRO B 44 VAL B 51 1 8 HELIX 9 9 SER B 57 ASN B 61 5 5 HELIX 10 10 GLY B 120 SER B 137 1 18 SHEET 1 A 7 LEU A 63 LEU A 65 0 SHEET 2 A 7 GLN A 68 SER A 76 -1 N CYS A 70 O LEU A 63 SHEET 3 A 7 SER A 84 THR A 89 -1 N ARG A 88 O SER A 71 SHEET 4 A 7 ASN A 99 LYS A 104 -1 N VAL A 102 O MET A 85 SHEET 5 A 7 THR A 108 GLY A 114 -1 N LEU A 112 O THR A 101 SHEET 6 A 7 CYS A 16 GLY A 23 -1 N VAL A 22 O LEU A 109 SHEET 7 A 7 SER A 29 ALA A 33 -1 N ALA A 32 O ILE A 21 SHEET 1 B 7 LEU B 63 LEU B 65 0 SHEET 2 B 7 GLN B 68 SER B 76 -1 N CYS B 70 O LEU B 63 SHEET 3 B 7 SER B 84 THR B 89 -1 N ARG B 88 O SER B 71 SHEET 4 B 7 ASN B 99 LYS B 104 -1 N VAL B 102 O MET B 85 SHEET 5 B 7 THR B 108 GLY B 114 -1 N LEU B 112 O THR B 101 SHEET 6 B 7 CYS B 16 GLY B 23 -1 N VAL B 22 O LEU B 109 SHEET 7 B 7 SER B 29 ALA B 33 -1 N ALA B 32 O ILE B 21 LINK CB7 HOM C 1 N PRO C 2 1555 1555 1.47 LINK CB7 HOM D 1 N PRO D 2 1555 1555 1.47 SITE 1 AC1 9 ASP A 8 MET A 11 ALA A 12 ASP A 26 SITE 2 AC1 9 SER A 27 PRO A 35 PRO A 44 PRO C 2 SITE 3 AC1 9 PRO C 3 SITE 1 AC2 10 ASP B 8 MET B 11 ALA B 12 ASP B 26 SITE 2 AC2 10 SER B 27 PRO B 35 PRO B 44 HOH B 500 SITE 3 AC2 10 PRO D 2 PRO D 3 CRYST1 105.400 51.800 77.500 90.00 131.10 90.00 C 1 2 1 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 0.009488 0.000000 0.008277 0.00000 SCALE2 0.000000 0.019305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017123 0.00000 MTRIX1 1 -0.066716 -0.003106 0.997767 58.83770 1 MTRIX2 1 -0.003460 -0.999988 -0.003345 33.44360 1 MTRIX3 1 0.997766 -0.003675 0.066704 -49.50680 1