HEADER PROTEIN BINDING 28-MAY-03 1PGV TITLE STRUCTURAL GENOMICS OF CAENORHABDITIS ELEGANS: TROPOMODULIN C-TERMINAL TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TROPOMODULIN TMD-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 SYNONYM: TMD-1; TROPOMODULIN PROTEIN 1, ISOFORM A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS STRUCTURAL GENOMICS; TROPOMODULIN, PSI, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS, SECSG, PROTEIN KEYWDS 3 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.SYMERSKY,S.LU,S.LI,L.CHEN,E.MEEHAN,M.LUO,S.QIU,R.J.BUNZEL,D.LUO, AUTHOR 2 A.ARABASHI,L.A.NAGY,G.LIN,W.C.-H.LUAN,M.CARSON,R.GRAY,W.HUANG, AUTHOR 3 SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS (SECSG) REVDAT 6 16-AUG-23 1PGV 1 SEQADV REVDAT 5 11-OCT-17 1PGV 1 REMARK REVDAT 4 24-FEB-09 1PGV 1 VERSN REVDAT 3 01-FEB-05 1PGV 1 AUTHOR KEYWDS REMARK REVDAT 2 27-JUL-04 1PGV 1 JRNL REMARK REVDAT 1 10-JUN-03 1PGV 0 JRNL AUTH S.LU,J.SYMERSKY,S.LI,M.CARSON,L.CHEN,E.MEEHAN,M.LUO JRNL TITL STRUCTURAL GENOMICS OF CAENORHABDITIS ELEGANS: CRYSTAL JRNL TITL 2 STRUCTURE OF THE TROPOMODULIN C-TERMINAL DOMAIN JRNL REF PROTEINS V. 56 384 2004 JRNL REFN ISSN 0887-3585 JRNL PMID 15211521 JRNL DOI 10.1002/PROT.10597 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.DING,S.QIU,R.J.BUNZEL,D.LUO,A.ARABASHI,S.LU,J.SYMERSKY, REMARK 1 AUTH 2 L.A.NAGY,L.J.DELUCAS,S.LI,M.LUO REMARK 1 TITL PURIFICATION, NANOCRYSTALLIZATION AND PRELIMINARY X_RAY REMARK 1 TITL 2 ANALYSIS OF A C_TERMINAL PART OF TROPOMODULIN PROTEIN 1, REMARK 1 TITL 3 ISOFORM A, FROM CAENORHABDITIS ELEGANS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 1106 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444903008217 REMARK 1 REFERENCE 2 REMARK 1 AUTH I.KRIEGER,A.KOSTYUKOVA,A.YAMASHITA,Y.NITANAI,Y.MAEDA REMARK 1 TITL CRYSTAL STRUCTURE OF THE C-TERMINAL HALF OF TROPOMODULIN AND REMARK 1 TITL 2 STRUCTURAL BASIS OF ACTIN FILAMENT POINTED-END CAPPING REMARK 1 REF BIOPHYS.J. V. 83 2716 2002 REMARK 1 REFN ISSN 0006-3495 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 16153 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) : 0.209 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 786 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 : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 47 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 : 1333 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.50 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.203 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.750 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.470 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.809 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 45.83 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PGV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019313. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9840 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16153 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1IO0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR: 28% PEG400, 0.1 M KCL, 10 REMARK 280 MM MGCL2, 0.1 M TRIS, PH 8. PROTEIN SOLUTION: 13.7 MG/ML IN 10 REMARK 280 MM HEPES, PH 7.5. DROPS: 1 MICROLITER RESERVOIR + 1 MICROLITER REMARK 280 PROTEIN SOLUTION. VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 15.85300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.56600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.31050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.56600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.85300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.31050 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: 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 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 196 REMARK 465 SER A 197 REMARK 465 HIS A 198 REMARK 465 GLY A 199 REMARK 465 THR A 200 REMARK 465 THR A 201 REMARK 465 PHE A 202 REMARK 465 ASN A 203 REMARK 465 GLY A 204 REMARK 465 ILE A 205 REMARK 465 MET A 206 REMARK 465 GLN A 207 REMARK 465 SER A 208 REMARK 465 TYR A 209 REMARK 465 VAL A 210 REMARK 465 PRO A 211 REMARK 465 ARG A 212 REMARK 465 ILE A 213 REMARK 465 VAL A 214 REMARK 465 PRO A 215 REMARK 465 ASP A 216 REMARK 465 GLU A 217 REMARK 465 PRO A 218 REMARK 465 ASP A 219 REMARK 465 ASN A 220 REMARK 465 ASP A 221 REMARK 465 ASP A 389 REMARK 465 PRO A 390 REMARK 465 ASN A 391 REMARK 465 VAL A 392 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 ASN A 303 -152.29 -122.18 REMARK 500 ALA A 328 24.11 -153.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IO0 RELATED DB: PDB REMARK 900 CHICKEN TROPOMODULIN C-TERMINAL DOMAIN REMARK 900 RELATED ID: C06A5.7 RELATED DB: TARGETDB DBREF 1PGV A 196 392 UNP O01479 TMOD_CAEEL 196 392 SEQADV 1PGV GLY A 196 UNP O01479 GLU 196 CLONING ARTIFACT SEQADV 1PGV HIS A 198 UNP O01479 THR 198 CLONING ARTIFACT SEQRES 1 A 197 GLY SER HIS GLY THR THR PHE ASN GLY ILE MET GLN SER SEQRES 2 A 197 TYR VAL PRO ARG ILE VAL PRO ASP GLU PRO ASP ASN ASP SEQRES 3 A 197 THR ASP VAL GLU SER CYS ILE ASN ARG LEU ARG GLU ASP SEQRES 4 A 197 ASP THR ASP LEU LYS GLU VAL ASN ILE ASN ASN MET LYS SEQRES 5 A 197 ARG VAL SER LYS GLU ARG ILE ARG SER LEU ILE GLU ALA SEQRES 6 A 197 ALA CYS ASN SER LYS HIS ILE GLU LYS PHE SER LEU ALA SEQRES 7 A 197 ASN THR ALA ILE SER ASP SER GLU ALA ARG GLY LEU ILE SEQRES 8 A 197 GLU LEU ILE GLU THR SER PRO SER LEU ARG VAL LEU ASN SEQRES 9 A 197 VAL GLU SER ASN PHE LEU THR PRO GLU LEU LEU ALA ARG SEQRES 10 A 197 LEU LEU ARG SER THR LEU VAL THR GLN SER ILE VAL GLU SEQRES 11 A 197 PHE LYS ALA ASP ASN GLN ARG GLN SER VAL LEU GLY ASN SEQRES 12 A 197 GLN VAL GLU MET ASP MET MET MET ALA ILE GLU GLU ASN SEQRES 13 A 197 GLU SER LEU LEU ARG VAL GLY ILE SER PHE ALA SER MET SEQRES 14 A 197 GLU ALA ARG HIS ARG VAL SER GLU ALA LEU GLU ARG ASN SEQRES 15 A 197 TYR GLU ARG VAL ARG LEU ARG ARG LEU GLY LYS ASP PRO SEQRES 16 A 197 ASN VAL FORMUL 2 HOH *131(H2 O) HELIX 1 1 ASP A 223 GLU A 233 1 11 HELIX 2 2 SER A 250 CYS A 262 1 13 HELIX 3 3 SER A 278 ARG A 283 1 6 HELIX 4 4 GLY A 284 SER A 292 1 9 HELIX 5 5 THR A 306 THR A 317 1 12 HELIX 6 6 GLY A 337 ASN A 351 1 15 HELIX 7 7 SER A 363 LEU A 386 1 24 SHEET 1 A 5 GLU A 240 ASN A 242 0 SHEET 2 A 5 LYS A 269 SER A 271 1 O LYS A 269 N VAL A 241 SHEET 3 A 5 VAL A 297 ASN A 299 1 O VAL A 297 N PHE A 270 SHEET 4 A 5 GLU A 325 LYS A 327 1 O GLU A 325 N LEU A 298 SHEET 5 A 5 ARG A 356 GLY A 358 1 O GLY A 358 N PHE A 326 CRYST1 31.706 50.621 107.132 90.00 90.00 90.00 P 21 21 21 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 0.031540 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019755 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009334 0.00000