HEADER CYTOSOLIC PROTEIN 04-NOV-17 6EWL TITLE DANIO RERIO CEP120 FIRST C2 DOMAIN (C2A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CENTROSOMAL PROTEIN 120; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: CEP120; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA KEYWDS CENTRIOLE CENTROSOME BASAL BODY CILIA, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.VAN BREUGEL,C.AL-JASSAR REVDAT 3 01-MAY-24 6EWL 1 REMARK REVDAT 2 13-JUN-18 6EWL 1 JRNL REVDAT 1 02-MAY-18 6EWL 0 JRNL AUTH N.JOSEPH,C.AL-JASSAR,C.M.JOHNSON,A.ANDREEVA,D.D.BARNABAS, JRNL AUTH 2 S.M.V.FREUND,F.GERGELY,M.VAN BREUGEL JRNL TITL DISEASE-ASSOCIATED MUTATIONS IN CEP120 DESTABILIZE THE JRNL TITL 2 PROTEIN AND IMPAIR CILIOGENESIS. JRNL REF CELL REP V. 23 2805 2018 JRNL REFN ESSN 2211-1247 JRNL PMID 29847808 JRNL DOI 10.1016/J.CELREP.2018.04.100 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.110 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 47584 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2426 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 30.6100 - 3.5980 1.00 2681 135 0.1504 0.1708 REMARK 3 2 3.5980 - 2.8565 1.00 2650 142 0.1531 0.1758 REMARK 3 3 2.8565 - 2.4956 1.00 2713 132 0.1767 0.2338 REMARK 3 4 2.4956 - 2.2675 1.00 2648 170 0.1609 0.2097 REMARK 3 5 2.2675 - 2.1050 1.00 2642 166 0.1460 0.1872 REMARK 3 6 2.1050 - 1.9809 1.00 2649 154 0.1415 0.1967 REMARK 3 7 1.9809 - 1.8818 1.00 2670 154 0.1400 0.1815 REMARK 3 8 1.8818 - 1.7999 1.00 2669 138 0.1447 0.2181 REMARK 3 9 1.7999 - 1.7306 0.99 2636 161 0.1586 0.2483 REMARK 3 10 1.7306 - 1.6709 1.00 2688 124 0.1770 0.2227 REMARK 3 11 1.6709 - 1.6186 0.99 2649 143 0.1827 0.2566 REMARK 3 12 1.6186 - 1.5724 1.00 2638 162 0.1793 0.2225 REMARK 3 13 1.5724 - 1.5310 0.99 2677 130 0.2046 0.2410 REMARK 3 14 1.5310 - 1.4936 0.99 2692 120 0.2263 0.2503 REMARK 3 15 1.4936 - 1.4597 0.96 2583 139 0.2674 0.3015 REMARK 3 16 1.4597 - 1.4286 0.99 2617 144 0.2822 0.3765 REMARK 3 17 1.4286 - 1.4000 0.97 2656 112 0.2992 0.3851 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.70 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 1202 REMARK 3 ANGLE : 1.222 1638 REMARK 3 CHIRALITY : 0.108 189 REMARK 3 PLANARITY : 0.008 209 REMARK 3 DIHEDRAL : 21.204 478 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 6EWL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-13 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 : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25380 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 31.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: C2 DOMAIN HOMOLOGY MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 7.5 200 MM MGCL2 30 % REMARK 280 (V/V) PEG-400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 15.72950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.32950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.72000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.32950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.72950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.72000 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 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: 8580 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 ASP A 135 REMARK 465 ASN A 136 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 OE2 GLU A 90 O HOH A 201 2.08 REMARK 500 OD2 ASP A 83 O HOH A 202 2.16 REMARK 500 O PRO A -1 O HOH A 203 2.18 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 N GLY A -2 OD CSO A 53 4565 1.87 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 CSO A 53 55.24 39.66 REMARK 500 SER A 87 58.66 30.70 REMARK 500 ILE A 105 105.57 -55.87 REMARK 500 LEU A 122 -161.66 62.10 REMARK 500 LYS A 123 82.73 59.61 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6EWL A 1 136 UNP A0A0G2KI14_DANRE DBREF2 6EWL A A0A0G2KI14 1 136 SEQADV 6EWL GLY A -2 UNP A0A0G2KI1 EXPRESSION TAG SEQADV 6EWL PRO A -1 UNP A0A0G2KI1 EXPRESSION TAG SEQADV 6EWL HIS A 0 UNP A0A0G2KI1 EXPRESSION TAG SEQADV 6EWL HIS A 66 UNP A0A0G2KI1 LEU 66 CONFLICT SEQADV 6EWL GLN A 67 UNP A0A0G2KI1 SER 67 CONFLICT SEQADV 6EWL HIS A 68 UNP A0A0G2KI1 ARG 68 CONFLICT SEQRES 1 A 139 GLY PRO HIS MET ALA SER LYS SER GLU GLN LEU LEU ILE SEQRES 2 A 139 VAL VAL SER ILE LEU GLU GLY ARG GLN PHE PRO ARG SER SEQRES 3 A 139 PRO ARG LEU SER LEU VAL VAL GLU ALA ARG PHE ASP GLY SEQRES 4 A 139 GLU THR LEU SER THR ASP PRO VAL GLU HIS LYS GLU GLN SEQRES 5 A 139 PRO GLN PHE CSO THR GLU LEU ALA TRP GLU LEU ASP ARG SEQRES 6 A 139 ARG THR LEU HIS GLN HIS ARG LEU GLN ARG THR PRO ILE SEQRES 7 A 139 LYS LEU GLN CYS TYR ALA VAL ASP SER SER THR SER ALA SEQRES 8 A 139 ARG GLU SER VAL GLY TYR ILE VAL LEU ASP LEU ARG SER SEQRES 9 A 139 VAL GLN GLU ILE LYS GLN ALA PRO LYS TRP HIS PRO LEU SEQRES 10 A 139 LEU SER SER LYS TYR THR LYS LEU LYS PRO ALA LEU LEU SEQRES 11 A 139 ILE GLY MET ILE LEU GLU ASN ASP ASN MODRES 6EWL CSO A 53 CYS MODIFIED RESIDUE HET CSO A 53 7 HETNAM CSO S-HYDROXYCYSTEINE FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 HOH *154(H2 O) HELIX 1 AA1 ARG A 62 ARG A 72 1 11 SHEET 1 AA1 4 THR A 54 ASP A 61 0 SHEET 2 AA1 4 GLN A 7 ARG A 18 -1 N LEU A 8 O LEU A 60 SHEET 3 AA1 4 ALA A 125 GLU A 133 -1 O LEU A 127 N GLU A 16 SHEET 4 AA1 4 LYS A 110 PRO A 113 -1 N HIS A 112 O LEU A 126 SHEET 1 AA2 3 GLU A 37 SER A 40 0 SHEET 2 AA2 3 SER A 27 PHE A 34 -1 N ALA A 32 O LEU A 39 SHEET 3 AA2 3 VAL A 44 GLU A 45 -1 O VAL A 44 N LEU A 28 SHEET 1 AA3 4 GLU A 37 SER A 40 0 SHEET 2 AA3 4 SER 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 TYR A 80 N VAL A 29 SHEET 4 AA3 4 ALA A 88 ASP A 98 -1 O ALA A 88 N ASP A 83 LINK C PHE A 52 N CSO A 53 1555 1555 1.33 LINK C CSO A 53 N THR A 54 1555 1555 1.33 CRYST1 31.459 53.440 74.659 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 0.031787 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013394 0.00000