HEADER STRUCTURAL PROTEIN 17-JUL-23 8PUZ TITLE CRYSTAL STRUCTURE OF TROPOMYOSIN (CDC8) CABLES, CONFORMER 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TROPOMYOSIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 GENE: CDC8, SPAC27F1.02C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TROPOMYOSIN, CDC8, YEAST, OVERLAP COMPLEX, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.Y.A.REINKE,M.ZAHN,R.FEDOROV,D.J.MANSTEIN REVDAT 1 24-JUL-24 8PUZ 0 JRNL AUTH P.Y.A.REINKE,D.J.MANSTEIN JRNL TITL ATOMIC STRUCTURE OF CDC8 TROPOMYOSIN CABLES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16951 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 861 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 24.6300 - 3.9900 0.99 2676 122 0.2362 0.2652 REMARK 3 2 3.9900 - 3.1700 1.00 2677 165 0.2205 0.2704 REMARK 3 3 3.1700 - 2.7700 1.00 2667 155 0.2195 0.2906 REMARK 3 4 2.7700 - 2.5200 1.00 2671 137 0.2407 0.3013 REMARK 3 5 2.5200 - 2.3400 1.00 2694 126 0.2355 0.2813 REMARK 3 6 2.3400 - 2.2000 1.00 2705 156 0.2748 0.3383 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.184 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.08 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 : 0.002 2660 REMARK 3 ANGLE : 0.320 3550 REMARK 3 CHIRALITY : 0.021 400 REMARK 3 PLANARITY : 0.002 478 REMARK 3 DIHEDRAL : 14.960 1102 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -0.0004 -16.3960 21.7802 REMARK 3 T TENSOR REMARK 3 T11: 0.3116 T22: 0.3577 REMARK 3 T33: 0.3752 T12: -0.0248 REMARK 3 T13: 0.0289 T23: 0.0424 REMARK 3 L TENSOR REMARK 3 L11: 3.4093 L22: 5.4189 REMARK 3 L33: 1.9045 L12: -4.2159 REMARK 3 L13: 2.5032 L23: -3.1221 REMARK 3 S TENSOR REMARK 3 S11: -0.0880 S12: -0.0883 S13: 0.1534 REMARK 3 S21: 0.1045 S22: -0.0074 S23: -0.2696 REMARK 3 S31: 0.0207 S32: -0.0016 S33: 0.0948 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 8PUZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292131846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A 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 : 1.00 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SADABS REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16997 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 26.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M TRIS HCL PH 8.2, AND 45% MPD, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 298K 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 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: 7870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 B 2 -130.17 54.20 REMARK 500 REMARK 500 REMARK: NULL DBREF 8PUZ A 1 161 UNP Q02088 TPM_SCHPO 1 161 DBREF 8PUZ B 1 161 UNP Q02088 TPM_SCHPO 1 161 SEQRES 1 A 161 MET ASP LYS LEU ARG GLU LYS ILE ASN ALA ALA ARG ALA SEQRES 2 A 161 GLU THR ASP GLU ALA VAL ALA ARG ALA GLU ALA ALA GLU SEQRES 3 A 161 ALA LYS LEU LYS GLU VAL GLU LEU GLN LEU SER LEU LYS SEQRES 4 A 161 GLU GLN GLU TYR GLU SER LEU SER ARG LYS SER GLU ALA SEQRES 5 A 161 ALA GLU SER GLN LEU GLU GLU LEU GLU GLU GLU THR LYS SEQRES 6 A 161 GLN LEU ARG LEU LYS ALA ASP ASN GLU ASP ILE GLN LYS SEQRES 7 A 161 THR GLU ALA GLU GLN LEU SER ARG LYS VAL GLU LEU LEU SEQRES 8 A 161 GLU GLU GLU LEU GLU THR ASN ASP LYS LEU LEU ARG GLU SEQRES 9 A 161 THR THR GLU LYS MET ARG GLN THR ASP VAL LYS ALA GLU SEQRES 10 A 161 HIS PHE GLU ARG ARG VAL GLN SER LEU GLU ARG GLU ARG SEQRES 11 A 161 ASP ASP MET GLU GLN LYS LEU GLU GLU MET THR ASP LYS SEQRES 12 A 161 TYR THR LYS VAL LYS ALA GLU LEU ASP GLU VAL HIS GLN SEQRES 13 A 161 ALA LEU GLU ASP LEU SEQRES 1 B 161 MET ASP LYS LEU ARG GLU LYS ILE ASN ALA ALA ARG ALA SEQRES 2 B 161 GLU THR ASP GLU ALA VAL ALA ARG ALA GLU ALA ALA GLU SEQRES 3 B 161 ALA LYS LEU LYS GLU VAL GLU LEU GLN LEU SER LEU LYS SEQRES 4 B 161 GLU GLN GLU TYR GLU SER LEU SER ARG LYS SER GLU ALA SEQRES 5 B 161 ALA GLU SER GLN LEU GLU GLU LEU GLU GLU GLU THR LYS SEQRES 6 B 161 GLN LEU ARG LEU LYS ALA ASP ASN GLU ASP ILE GLN LYS SEQRES 7 B 161 THR GLU ALA GLU GLN LEU SER ARG LYS VAL GLU LEU LEU SEQRES 8 B 161 GLU GLU GLU LEU GLU THR ASN ASP LYS LEU LEU ARG GLU SEQRES 9 B 161 THR THR GLU LYS MET ARG GLN THR ASP VAL LYS ALA GLU SEQRES 10 B 161 HIS PHE GLU ARG ARG VAL GLN SER LEU GLU ARG GLU ARG SEQRES 11 B 161 ASP ASP MET GLU GLN LYS LEU GLU GLU MET THR ASP LYS SEQRES 12 B 161 TYR THR LYS VAL LYS ALA GLU LEU ASP GLU VAL HIS GLN SEQRES 13 B 161 ALA LEU GLU ASP LEU FORMUL 3 HOH *35(H2 O) HELIX 1 AA1 MET A 1 LEU A 161 1 161 HELIX 2 AA2 ASP B 2 ASP B 72 1 71 HELIX 3 AA3 ASN B 73 ASP B 160 1 88 CRYST1 23.267 38.616 98.933 94.31 91.92 102.94 P 1 2 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 0.042979 0.009875 0.002287 0.00000 SCALE2 0.000000 0.026571 0.002263 0.00000 SCALE3 0.000000 0.000000 0.010150 0.00000