HEADER PROTEIN BINDING 14-DEC-00 1IO0 TITLE CRYSTAL STRUCTURE OF TROPOMODULIN C-TERMINAL HALF COMPND MOL_ID: 1; COMPND 2 MOLECULE: TROPOMODULIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET(HIS)TMOD KEYWDS LRR PROTEIN, RIGHT-HANDED SUPER-HELIX, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR I.KRIEGER,A.KOSTYUKOVA,A.YAMASHITA,Y.MAEDA REVDAT 4 27-DEC-23 1IO0 1 REMARK LINK REVDAT 3 23-OCT-19 1IO0 1 JRNL REVDAT 2 24-FEB-09 1IO0 1 VERSN REVDAT 1 27-NOV-02 1IO0 0 JRNL AUTH I.KRIEGER,A.KOSTYUKOVA,A.YAMASHITA,Y.NITANAI,Y.MAEDA JRNL TITL CRYSTAL STRUCTURE OF THE C-TERMINAL HALF OF TROPOMODULIN AND JRNL TITL 2 STRUCTURAL BASIS OF ACTIN FILAMENT POINTED-END CAPPING. JRNL REF BIOPHYS.J. V. 83 2716 2002 JRNL REFN ISSN 0006-3495 JRNL PMID 12414704 JRNL DOI 10.1016/S0006-3495(02)75281-8 REMARK 2 REMARK 2 RESOLUTION. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 31866 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) : 0.203 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 : 1602 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3641 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.14 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 165 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 : 1297 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 231 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.89 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.052 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.07 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.566 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) : 1.003 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.587 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.412 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.959 ; 2.500 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 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO.TOP REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE PROGRAM REFMAC (CCP4) WAS ALSO USED REMARK 3 IN REFINEMENT PROCESS FOR DATA AT 20.0-1.45 A REMARK 4 REMARK 4 1IO0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-DEC-00. REMARK 100 THE DEPOSITION ID IS D_1000005107. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31954 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28600 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: MAD REMARK 200 SOFTWARE USED: SOLVE, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, ZINC SULFATE, MES, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 34.64700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.00345 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.74100 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 34.64700 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 20.00345 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.74100 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 34.64700 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 20.00345 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.74100 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.00691 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 67.48200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 40.00691 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 67.48200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 40.00691 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 67.48200 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 160 REMARK 465 LEU A 161 REMARK 465 ASN A 162 REMARK 465 SER A 163 REMARK 465 VAL A 164 REMARK 465 ILE A 165 REMARK 465 LYS A 166 REMARK 465 PRO A 167 REMARK 465 THR A 168 REMARK 465 LYS A 169 REMARK 465 TYR A 170 REMARK 465 LYS A 171 REMARK 465 PRO A 172 REMARK 465 VAL A 173 REMARK 465 PRO A 174 REMARK 465 ASP A 175 REMARK 465 GLU A 176 REMARK 465 GLU A 177 REMARK 465 PRO A 178 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 262 -160.60 -129.86 REMARK 500 TYR A 317 143.93 -175.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 ZN IS ALSO COORDINATED WITH OD2 ASP 194 AND REMARK 600 OD2 ASP 196 IN A SYMMTERY_RELATED MOLECULE. REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 194 OD2 REMARK 620 2 ASP A 196 OD1 75.0 REMARK 620 3 ASP A 196 OD2 118.1 53.0 REMARK 620 4 ASP A 288 OD1 117.9 143.1 93.2 REMARK 620 5 HIS A 318 ND1 106.6 102.6 114.7 105.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 DBREF 1IO0 A 160 344 UNP Q9DEA6 Q9DEA6_CHICK 146 330 SEQRES 1 A 185 GLY LEU ASN SER VAL ILE LYS PRO THR LYS TYR LYS PRO SEQRES 2 A 185 VAL PRO ASP GLU GLU PRO ASN SER THR ASP VAL GLU GLU SEQRES 3 A 185 THR LEU LYS ARG ILE GLN ASN ASN ASP PRO ASP LEU GLU SEQRES 4 A 185 GLU VAL ASN LEU ASN ASN ILE MET ASN ILE PRO VAL PRO SEQRES 5 A 185 THR LEU LYS ALA CYS ALA GLU ALA LEU LYS THR ASN THR SEQRES 6 A 185 TYR VAL LYS LYS PHE SER ILE VAL GLY THR ARG SER ASN SEQRES 7 A 185 ASP PRO VAL ALA PHE ALA LEU ALA GLU MET LEU LYS VAL SEQRES 8 A 185 ASN ASN THR LEU LYS SER LEU ASN VAL GLU SER ASN PHE SEQRES 9 A 185 ILE SER GLY SER GLY ILE LEU ALA LEU VAL GLU ALA LEU SEQRES 10 A 185 GLN SER ASN THR SER LEU ILE GLU LEU ARG ILE ASP ASN SEQRES 11 A 185 GLN SER GLN PRO LEU GLY ASN ASN VAL GLU MET GLU ILE SEQRES 12 A 185 ALA ASN MET LEU GLU LYS ASN THR THR LEU LEU LYS PHE SEQRES 13 A 185 GLY TYR HIS PHE THR GLN GLN GLY PRO ARG LEU ARG ALA SEQRES 14 A 185 SER ASN ALA MET MET ASN ASN ASN ASP LEU VAL ARG LYS SEQRES 15 A 185 ARG ARG LEU HET ZN A1001 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *231(H2 O) HELIX 1 1 ASP A 182 ASN A 192 1 11 HELIX 2 2 PRO A 209 LYS A 221 1 13 HELIX 3 3 ASN A 237 LYS A 249 1 13 HELIX 4 4 SER A 265 ALA A 275 1 11 HELIX 5 5 LEU A 276 ASN A 279 5 4 HELIX 6 6 GLY A 295 LYS A 308 1 14 HELIX 7 7 GLN A 321 ARG A 343 1 23 SHEET 1 A 5 GLU A 199 ASN A 201 0 SHEET 2 A 5 LYS A 228 SER A 230 1 O LYS A 228 N VAL A 200 SHEET 3 A 5 SER A 256 ASN A 258 1 O SER A 256 N PHE A 229 SHEET 4 A 5 GLU A 284 ARG A 286 1 O GLU A 284 N LEU A 257 SHEET 5 A 5 LYS A 314 GLY A 316 1 O LYS A 314 N LEU A 285 LINK OD2 ASP A 194 ZN ZN A1001 6455 1555 1.94 LINK OD1 ASP A 196 ZN ZN A1001 6455 1555 2.70 LINK OD2 ASP A 196 ZN ZN A1001 6455 1555 2.01 LINK OD1 ASP A 288 ZN ZN A1001 1555 1555 2.06 LINK ND1 HIS A 318 ZN ZN A1001 1555 1555 2.03 SITE 1 AC1 4 ASP A 194 ASP A 196 ASP A 288 HIS A 318 CRYST1 69.294 69.294 101.223 90.00 90.00 120.00 H 3 9 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 0.014431 0.008332 0.000000 0.00000 SCALE2 0.000000 0.016664 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009879 0.00000