HEADER STRUCTURAL PROTEIN 26-JAN-18 6FLJ TITLE CRYSTAL STRUCTURE OF CEP120 C2A_K76A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CENTROSOMAL PROTEIN OF 120 KDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CEP120,COILED-COIL DOMAIN-CONTAINING PROTEIN 100; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CEP120, CCDC100; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CENTRIOLE, MICROTUBULE, CEP120, C2 DOMAIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SHARMA,S.F.GERARD,N.OLIERIC,M.O.STEINMETZ REVDAT 3 17-JAN-24 6FLJ 1 REMARK REVDAT 2 06-JUN-18 6FLJ 1 JRNL REVDAT 1 14-FEB-18 6FLJ 0 JRNL AUTH A.SHARMA,S.F.GERARD,N.OLIERIC,M.O.STEINMETZ JRNL TITL CEP120 PROMOTES MICROTUBULE FORMATION THROUGH A UNIQUE JRNL TITL 2 TUBULIN BINDING C2 DOMAIN. JRNL REF J. STRUCT. BIOL. V. 203 62 2018 JRNL REFN ESSN 1095-8657 JRNL PMID 29398280 JRNL DOI 10.1016/J.JSB.2018.01.009 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2863: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14675 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1372 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 40.7212 - 3.7707 1.00 2597 137 0.1800 0.2253 REMARK 3 2 3.7707 - 2.9932 1.00 2608 133 0.1915 0.2130 REMARK 3 3 2.9932 - 2.6149 1.00 2571 136 0.2199 0.2521 REMARK 3 4 2.6149 - 2.3759 1.00 2618 140 0.2415 0.2865 REMARK 3 5 2.3759 - 2.2056 1.00 2608 141 0.2114 0.2431 REMARK 3 6 2.2056 - 2.0755 1.00 2576 137 0.2121 0.2612 REMARK 3 7 2.0755 - 1.9716 1.00 2601 138 0.2253 0.2704 REMARK 3 8 1.9716 - 1.8858 1.00 2585 139 0.2791 0.3006 REMARK 3 9 1.8858 - 1.8132 1.00 2592 137 0.3092 0.3294 REMARK 3 10 1.8132 - 1.7506 0.98 2534 134 0.3712 0.3765 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.79 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 : 0.012 1057 REMARK 3 ANGLE : 1.243 1434 REMARK 3 CHIRALITY : 0.073 165 REMARK 3 PLANARITY : 0.006 182 REMARK 3 DIHEDRAL : 17.686 399 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 53 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.0978 8.5578 -8.3913 REMARK 3 T TENSOR REMARK 3 T11: 0.2495 T22: 0.3373 REMARK 3 T33: 0.2604 T12: -0.0236 REMARK 3 T13: 0.0137 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 3.3605 L22: 2.9141 REMARK 3 L33: 3.1082 L12: 0.7341 REMARK 3 L13: 1.2878 L23: 2.0945 REMARK 3 S TENSOR REMARK 3 S11: -0.0707 S12: -0.0790 S13: -0.0640 REMARK 3 S21: -0.0406 S22: -0.0276 S23: 0.2025 REMARK 3 S31: 0.0560 S32: -0.1324 S33: 0.0290 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 54 THROUGH 135 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.7628 8.3856 -16.9988 REMARK 3 T TENSOR REMARK 3 T11: 0.3566 T22: 0.4523 REMARK 3 T33: 0.3149 T12: 0.0114 REMARK 3 T13: -0.0327 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 3.2969 L22: 2.1088 REMARK 3 L33: 3.1059 L12: 0.3840 REMARK 3 L13: 1.9768 L23: 0.8624 REMARK 3 S TENSOR REMARK 3 S11: 0.0775 S12: 0.4891 S13: -0.1164 REMARK 3 S21: -0.4425 S22: -0.0194 S23: 0.1612 REMARK 3 S31: 0.0152 S32: 0.2148 S33: -0.0191 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 6FLJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200007881. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-17 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14678 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 40.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.06880 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 12.20 REMARK 200 R MERGE FOR SHELL (I) : 1.92500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.290 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4ICW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350 AND 0.2 M NASCN, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 20.42100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.37850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.68350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.37850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.42100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.68350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 -1 REMARK 465 PRO A 0 REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 SER A 5 REMARK 465 GLN A 103 REMARK 465 GLU A 104 REMARK 465 THR A 105 REMARK 465 THR A 136 REMARK 465 LYS A 137 REMARK 465 PRO A 138 REMARK 465 PRO A 139 REMARK 465 VAL A 140 REMARK 465 ASP A 141 REMARK 465 SER A 142 REMARK 465 PHE A 143 REMARK 465 LYS A 144 REMARK 465 ALA A 145 REMARK 465 LYS A 146 REMARK 465 GLY A 147 REMARK 465 ALA A 148 REMARK 465 PRO A 149 REMARK 465 PRO A 150 REMARK 465 ARG A 151 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 LEU A 15 -95.49 -100.93 REMARK 500 ASP A 35 50.19 39.27 REMARK 500 GLN A 49 78.03 -117.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 279 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 280 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A 281 DISTANCE = 8.07 ANGSTROMS DBREF 6FLJ A 1 151 UNP Q8N960 CE120_HUMAN 1 151 SEQADV 6FLJ GLY A -1 UNP Q8N960 EXPRESSION TAG SEQADV 6FLJ PRO A 0 UNP Q8N960 EXPRESSION TAG SEQADV 6FLJ ALA A 76 UNP Q8N960 LYS 76 ENGINEERED MUTATION SEQRES 1 A 153 GLY PRO MET VAL SER LYS SER ASP GLN LEU LEU ILE VAL SEQRES 2 A 153 VAL SER ILE LEU GLU GLY ARG HIS PHE PRO LYS ARG PRO SEQRES 3 A 153 LYS HIS MET LEU VAL VAL GLU ALA LYS PHE ASP GLY GLU SEQRES 4 A 153 GLN LEU ALA THR ASP PRO VAL ASP HIS THR ASP GLN PRO SEQRES 5 A 153 GLU PHE ALA THR GLU LEU ALA TRP GLU ILE ASP ARG LYS SEQRES 6 A 153 ALA LEU HIS GLN HIS ARG LEU GLN ARG THR PRO ILE ALA SEQRES 7 A 153 LEU GLN CYS PHE ALA LEU ASP PRO VAL THR SER ALA LYS SEQRES 8 A 153 GLU THR ILE GLY TYR ILE VAL LEU ASP LEU ARG THR ALA SEQRES 9 A 153 GLN GLU THR LYS GLN ALA PRO LYS TRP TYR GLN LEU LEU SEQRES 10 A 153 SER ASN LYS TYR THR LYS PHE LYS SER GLU ILE GLN ILE SEQRES 11 A 153 SER ILE ALA LEU GLU THR ASP THR LYS PRO PRO VAL ASP SEQRES 12 A 153 SER PHE LYS ALA LYS GLY ALA PRO PRO ARG FORMUL 2 HOH *81(H2 O) HELIX 1 AA1 ASP A 61 ARG A 72 1 12 HELIX 2 AA2 ARG A 100 ALA A 102 5 3 SHEET 1 AA1 4 GLU A 51 ILE A 60 0 SHEET 2 AA1 4 LEU A 8 ARG A 18 -1 N VAL A 12 O LEU A 56 SHEET 3 AA1 4 GLU A 125 THR A 134 -1 O GLU A 133 N LEU A 9 SHEET 4 AA1 4 LYS A 110 GLN A 113 -1 N LYS A 110 O ILE A 128 SHEET 1 AA2 3 GLU A 37 ALA A 40 0 SHEET 2 AA2 3 MET A 27 PHE A 34 -1 N ALA A 32 O LEU A 39 SHEET 3 AA2 3 VAL A 44 ASP A 45 -1 O VAL A 44 N LEU A 28 SHEET 1 AA3 4 GLU A 37 ALA A 40 0 SHEET 2 AA3 4 MET A 27 PHE A 34 -1 N ALA A 32 O LEU A 39 SHEET 3 AA3 4 PRO A 74 ASP A 83 -1 O LEU A 82 N MET A 27 SHEET 4 AA3 4 ALA A 88 ASP A 98 -1 O ILE A 92 N CYS A 79 CRYST1 40.842 51.367 66.757 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 0.024485 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019468 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014980 0.00000