HEADER ACTIN-BINDING PROTEIN 15-JUN-16 5KHT TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL FRAGMENT OF TROPOMYOSIN ISOFORM TITLE 2 TPM1.1 AT 1.5 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TROPOMYOSIN ALPHA-1 CHAIN,GENERAL CONTROL PROTEIN GCN4; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: ALPHA-TROPOMYOSIN,TROPOMYOSIN-1,AMINO ACID BIOSYNTHESIS COMPND 5 REGULATORY PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: HUMAN, BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 9606, 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: TPM1, C15ORF13, TMSA, GCN4, AAS3, ARG9, YEL009C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TROPOMYOSIN, COILED COIL, ACTIN-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.S.KOSTYUKOVA,I.KRIEGER,Y.-H.YOON,D.TOLKATCHEV,F.A.SAMATEY REVDAT 5 03-APR-24 5KHT 1 REMARK REVDAT 4 06-MAR-24 5KHT 1 REMARK REVDAT 3 02-JAN-19 5KHT 1 JRNL REVDAT 2 06-SEP-17 5KHT 1 REMARK REVDAT 1 21-JUN-17 5KHT 0 JRNL AUTH T.LY,I.KRIEGER,D.TOLKATCHEV,C.KRONE,T.MOURAL,F.A.SAMATEY, JRNL AUTH 2 C.KANG,A.S.KOSTYUKOVA JRNL TITL STRUCTURAL DESTABILIZATION OF TROPOMYOSIN INDUCED BY THE JRNL TITL 2 CARDIOMYOPATHY-LINKED MUTATION R21H. JRNL REF PROTEIN SCI. V. 27 498 2018 JRNL REFN ESSN 1469-896X JRNL PMID 29105867 JRNL DOI 10.1002/PRO.3341 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.1 REMARK 3 NUMBER OF REFLECTIONS : 21830 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1986 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 34.5583 - 3.6053 0.92 1568 157 0.1837 0.1806 REMARK 3 2 3.6053 - 2.8621 0.93 1597 147 0.1903 0.2512 REMARK 3 3 2.8621 - 2.5004 0.90 1533 160 0.2064 0.2755 REMARK 3 4 2.5004 - 2.2718 0.93 1573 155 0.2003 0.2362 REMARK 3 5 2.2718 - 2.1090 0.88 1500 149 0.1931 0.2232 REMARK 3 6 2.1090 - 1.9847 0.91 1540 154 0.2059 0.2904 REMARK 3 7 1.9847 - 1.8853 0.93 1587 156 0.2425 0.3152 REMARK 3 8 1.8853 - 1.8033 0.87 1469 155 0.2473 0.2907 REMARK 3 9 1.8033 - 1.7338 0.89 1528 150 0.2437 0.2660 REMARK 3 10 1.7338 - 1.6740 0.91 1545 161 0.2453 0.3408 REMARK 3 11 1.6740 - 1.6217 0.91 1556 153 0.2499 0.3684 REMARK 3 12 1.6217 - 1.5753 0.72 1208 118 0.2594 0.3343 REMARK 3 13 1.5753 - 1.5338 0.55 938 90 0.2702 0.2946 REMARK 3 14 1.5338 - 1.4964 0.41 702 81 0.2833 0.4028 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.310 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) : 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 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 : 0.007 1608 REMARK 3 ANGLE : 1.011 2122 REMARK 3 CHIRALITY : 0.066 225 REMARK 3 PLANARITY : 0.004 279 REMARK 3 DIHEDRAL : 16.934 686 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 5KHT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222240. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS V.2015 REMARK 200 DATA SCALING SOFTWARE : XSCALE NOVEMBER 3, 2014 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21841 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.496 REMARK 200 RESOLUTION RANGE LOW (A) : 34.549 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.1 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41200 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: PHASER V2.5.6 REMARK 200 STARTING MODEL: CHIMERIC MODEL BUILT BY PHYRE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, HEPES/SODIUM HYDROXIDE, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 14 O HOH A 101 2.14 REMARK 500 NZ LYS B 5 O HOH B 201 2.15 REMARK 500 O GLY B -1 O HOH B 202 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 46 OD1 ASP C 20 1565 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 D 2 3.53 -64.58 REMARK 500 ILE D 4 -36.93 -36.68 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 PEG B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG D 101 DBREF 5KHT A 1 28 UNP P09493 TPM1_HUMAN 1 28 DBREF 5KHT A 29 46 UNP P03069 GCN4_YEAST 264 281 DBREF 5KHT B 1 28 UNP P09493 TPM1_HUMAN 1 28 DBREF 5KHT B 29 46 UNP P03069 GCN4_YEAST 264 281 DBREF 5KHT C 1 28 UNP P09493 TPM1_HUMAN 1 28 DBREF 5KHT C 29 46 UNP P03069 GCN4_YEAST 264 281 DBREF 5KHT D 1 28 UNP P09493 TPM1_HUMAN 1 28 DBREF 5KHT D 29 46 UNP P03069 GCN4_YEAST 264 281 SEQADV 5KHT GLY A -1 UNP P09493 EXPRESSION TAG SEQADV 5KHT GLY B -1 UNP P09493 EXPRESSION TAG SEQADV 5KHT GLY C -1 UNP P09493 EXPRESSION TAG SEQADV 5KHT GLY D -1 UNP P09493 EXPRESSION TAG SEQRES 1 A 47 GLY MET ASP ALA ILE LYS LYS LYS MET GLN MET LEU LYS SEQRES 2 A 47 LEU ASP LYS GLU ASN ALA LEU ASP ARG ALA GLU GLN ALA SEQRES 3 A 47 GLU ALA ASP ASN TYR HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 4 A 47 LEU LYS LYS LEU VAL GLY GLU ARG SEQRES 1 B 47 GLY MET ASP ALA ILE LYS LYS LYS MET GLN MET LEU LYS SEQRES 2 B 47 LEU ASP LYS GLU ASN ALA LEU ASP ARG ALA GLU GLN ALA SEQRES 3 B 47 GLU ALA ASP ASN TYR HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 4 B 47 LEU LYS LYS LEU VAL GLY GLU ARG SEQRES 1 C 47 GLY MET ASP ALA ILE LYS LYS LYS MET GLN MET LEU LYS SEQRES 2 C 47 LEU ASP LYS GLU ASN ALA LEU ASP ARG ALA GLU GLN ALA SEQRES 3 C 47 GLU ALA ASP ASN TYR HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 4 C 47 LEU LYS LYS LEU VAL GLY GLU ARG SEQRES 1 D 47 GLY MET ASP ALA ILE LYS LYS LYS MET GLN MET LEU LYS SEQRES 2 D 47 LEU ASP LYS GLU ASN ALA LEU ASP ARG ALA GLU GLN ALA SEQRES 3 D 47 GLU ALA ASP ASN TYR HIS LEU GLU ASN GLU VAL ALA ARG SEQRES 4 D 47 LEU LYS LYS LEU VAL GLY GLU ARG HET PEG B 101 7 HET PEG C 101 7 HET PEG C 102 7 HET PEG D 101 7 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 5 PEG 4(C4 H10 O3) FORMUL 9 HOH *169(H2 O) HELIX 1 AA1 GLY A -1 GLY A 44 1 45 HELIX 2 AA2 MET B 1 GLY B 44 1 44 HELIX 3 AA3 MET C 1 GLY C 44 1 44 HELIX 4 AA4 ALA D 3 GLY D 44 1 42 SITE 1 AC1 9 ASP B 14 VAL B 36 ALA B 37 LYS B 40 SITE 2 AC1 9 HOH B 203 HOH B 210 HOH B 217 HOH B 232 SITE 3 AC1 9 LYS D 15 SITE 1 AC2 7 GLY B 44 GLU B 45 HOH B 212 LYS C 12 SITE 2 AC2 7 LEU C 13 PEG C 102 GLU D 23 SITE 1 AC3 4 GLU B 45 ARG B 46 GLN C 9 PEG C 101 SITE 1 AC4 7 ARG A 38 LEU A 42 VAL C 43 GLY C 44 SITE 2 AC4 7 ARG C 46 GLU D 45 HOH D 203 CRYST1 35.970 36.470 36.710 65.21 74.71 78.98 P 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 0.027801 -0.005413 -0.005965 0.00000 SCALE2 0.000000 0.027935 -0.011817 0.00000 SCALE3 0.000000 0.000000 0.030664 0.00000