HEADER UNKNOWN FUNCTION 25-SEP-08 3ENC TITLE CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS PCC1 DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN PCC1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PCC1; COMPND 5 SYNONYM: UNCHARACTERIZED PROTEIN PF2011; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 STRAIN: DSM 3638; SOURCE 5 GENE: PF2011; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS DIMERIZATION DOMAIN, KEOPS, TELOMERE, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR D.NECULAI REVDAT 5 30-OCT-24 3ENC 1 REMARK REVDAT 4 20-OCT-21 3ENC 1 SEQADV LINK REVDAT 3 12-JAN-10 3ENC 1 JRNL REVDAT 2 24-FEB-09 3ENC 1 VERSN REVDAT 1 28-OCT-08 3ENC 0 JRNL AUTH D.Y.MAO,D.NECULAI,M.DOWNEY,S.ORLICKY,Y.Z.HAFFANI, JRNL AUTH 2 D.F.CECCARELLI,J.S.HO,R.K.SZILARD,W.ZHANG,C.S.HO,L.WAN, JRNL AUTH 3 C.FARES,S.RUMPEL,I.KURINOV,C.H.ARROWSMITH,D.DUROCHER, JRNL AUTH 4 F.SICHERI JRNL TITL ATOMIC STRUCTURE OF THE KEOPS COMPLEX: AN ANCIENT PROTEIN JRNL TITL 2 KINASE-CONTAINING MOLECULAR MACHINE. JRNL REF MOL.CELL V. 32 259 2008 JRNL REFN ISSN 1097-2765 JRNL PMID 18951093 JRNL DOI 10.1016/J.MOLCEL.2008.10.002 REMARK 2 REMARK 2 RESOLUTION. 2.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 6390 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.010 REMARK 3 FREE R VALUE TEST SET COUNT : 448 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 68.2744 - 3.7935 0.98 1998 151 0.1611 0.2001 REMARK 3 2 3.7935 - 3.0110 0.98 1978 149 0.2390 0.2576 REMARK 3 3 3.0110 - 2.6304 0.98 1966 148 0.2792 0.2882 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 : 0.36 REMARK 3 B_SOL : 138.4 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : -1.20710 REMARK 3 B22 (A**2) : -1.20710 REMARK 3 B33 (A**2) : -39.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.5030 REMARK 3 OPERATOR: H,-H-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 1296 REMARK 3 ANGLE : 1.232 1744 REMARK 3 CHIRALITY : 0.082 202 REMARK 3 PLANARITY : 0.005 214 REMARK 3 DIHEDRAL : 20.158 488 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): 14.1503 24.3766 30.0971 REMARK 3 T TENSOR REMARK 3 T11: 0.3106 T22: 0.7629 REMARK 3 T33: 0.5327 T12: 0.1763 REMARK 3 T13: 0.0666 T23: -0.0937 REMARK 3 L TENSOR REMARK 3 L11: -0.2760 L22: 1.5026 REMARK 3 L33: 3.6317 L12: 1.3019 REMARK 3 L13: -2.5519 L23: 0.8468 REMARK 3 S TENSOR REMARK 3 S11: -0.0849 S12: 0.2239 S13: -0.4186 REMARK 3 S21: 0.1051 S22: 0.2156 S23: 0.0218 REMARK 3 S31: 0.0114 S32: -0.2511 S33: -0.1099 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 3ENC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000049538. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97935 REMARK 200 MONOCHROMATOR : HORIZONTAL BENT SI(111), REMARK 200 ASYMMETRICALLY CUT WITH WATER REMARK 200 COOLED CU BLOCK REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6401 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.630 REMARK 200 RESOLUTION RANGE LOW (A) : 68.251 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.480 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 1.930 REMARK 200 R MERGE (I) : 0.03310 REMARK 200 R SYM (I) : 0.03050 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.93 REMARK 200 R MERGE FOR SHELL (I) : 0.26770 REMARK 200 R SYM FOR SHELL (I) : 0.39800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% PEG 300 0.1 M NA/K PHOSPHATE, PH REMARK 280 6.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.01000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.01000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.01000 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: 2470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 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 -4 REMARK 465 ALA A -3 REMARK 465 MSE A -2 REMARK 465 ASP A -1 REMARK 465 PRO A 0 REMARK 465 MSE A 1 REMARK 465 GLU A 81 REMARK 465 VAL A 82 REMARK 465 GLY B -4 REMARK 465 ALA B -3 REMARK 465 MSE B -2 REMARK 465 ASP B -1 REMARK 465 PRO B 0 REMARK 465 MSE B 1 REMARK 465 GLU B 81 REMARK 465 VAL B 82 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 LYS A 4 -113.04 -100.06 REMARK 500 PRO A 15 -81.12 -64.89 REMARK 500 TYR A 36 42.69 88.22 REMARK 500 ALA A 61 -7.37 -57.41 REMARK 500 PRO B 15 -88.38 -41.45 REMARK 500 GLU B 17 2.58 -59.52 REMARK 500 SER B 39 -79.46 -94.45 REMARK 500 VAL B 79 59.84 -110.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EN9 RELATED DB: PDB REMARK 900 RELATED ID: 3ENH RELATED DB: PDB REMARK 900 RELATED ID: 3ENO RELATED DB: PDB DBREF 3ENC A 1 82 UNP Q8TZI1 Q8TZI1_PYRFU 1 82 DBREF 3ENC B 1 82 UNP Q8TZI1 Q8TZI1_PYRFU 1 82 SEQADV 3ENC GLY A -4 UNP Q8TZI1 EXPRESSION TAG SEQADV 3ENC ALA A -3 UNP Q8TZI1 EXPRESSION TAG SEQADV 3ENC MSE A -2 UNP Q8TZI1 EXPRESSION TAG SEQADV 3ENC ASP A -1 UNP Q8TZI1 EXPRESSION TAG SEQADV 3ENC PRO A 0 UNP Q8TZI1 EXPRESSION TAG SEQADV 3ENC MSE A 12 UNP Q8TZI1 ILE 12 ENGINEERED MUTATION SEQADV 3ENC GLY B -4 UNP Q8TZI1 EXPRESSION TAG SEQADV 3ENC ALA B -3 UNP Q8TZI1 EXPRESSION TAG SEQADV 3ENC MSE B -2 UNP Q8TZI1 EXPRESSION TAG SEQADV 3ENC ASP B -1 UNP Q8TZI1 EXPRESSION TAG SEQADV 3ENC PRO B 0 UNP Q8TZI1 EXPRESSION TAG SEQADV 3ENC MSE B 12 UNP Q8TZI1 ILE 12 ENGINEERED MUTATION SEQRES 1 A 87 GLY ALA MSE ASP PRO MSE LYS ALA LYS ARG VAL GLN ALA SEQRES 2 A 87 LYS ILE GLU MSE GLU PHE PRO SER GLU ASP VAL ALA LYS SEQRES 3 A 87 VAL VAL TYR GLU ALA VAL LEU TYR GLU HIS LEU SER VAL SEQRES 4 A 87 PRO TYR ARG ARG SER GLU ILE ASP PHE LYS LEU GLU GLY SEQRES 5 A 87 LYS LYS ILE ILE LEU ASP ILE LYS ALA THR ASP SER SER SEQRES 6 A 87 ALA LEU ARG GLY THR VAL ASN SER TYR LEU ARG TRP ILE SEQRES 7 A 87 LYS ALA ALA ILE ASP VAL ILE GLU VAL SEQRES 1 B 87 GLY ALA MSE ASP PRO MSE LYS ALA LYS ARG VAL GLN ALA SEQRES 2 B 87 LYS ILE GLU MSE GLU PHE PRO SER GLU ASP VAL ALA LYS SEQRES 3 B 87 VAL VAL TYR GLU ALA VAL LEU TYR GLU HIS LEU SER VAL SEQRES 4 B 87 PRO TYR ARG ARG SER GLU ILE ASP PHE LYS LEU GLU GLY SEQRES 5 B 87 LYS LYS ILE ILE LEU ASP ILE LYS ALA THR ASP SER SER SEQRES 6 B 87 ALA LEU ARG GLY THR VAL ASN SER TYR LEU ARG TRP ILE SEQRES 7 B 87 LYS ALA ALA ILE ASP VAL ILE GLU VAL MODRES 3ENC MSE A 12 MET SELENOMETHIONINE MODRES 3ENC MSE B 12 MET SELENOMETHIONINE HET MSE A 12 8 HET MSE B 12 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) HELIX 1 1 SER A 16 LEU A 28 1 13 HELIX 2 2 LEU A 28 SER A 33 1 6 HELIX 3 3 ASP A 58 ASP A 78 1 21 HELIX 4 4 VAL B 19 SER B 33 1 15 HELIX 5 5 ASP B 58 ASP B 78 1 21 SHEET 1 A 3 GLU A 40 ILE A 41 0 SHEET 2 A 3 LYS A 49 ALA A 56 -1 O LYS A 55 N GLU A 40 SHEET 3 A 3 LYS A 44 LEU A 45 -1 N LYS A 44 O ILE A 51 SHEET 1 B 6 GLU A 40 ILE A 41 0 SHEET 2 B 6 LYS A 49 ALA A 56 -1 O LYS A 55 N GLU A 40 SHEET 3 B 6 VAL A 6 GLU A 13 -1 N ILE A 10 O LEU A 52 SHEET 4 B 6 VAL B 6 GLU B 13 -1 O GLN B 7 N GLU A 11 SHEET 5 B 6 LYS B 49 ALA B 56 -1 O ALA B 56 N VAL B 6 SHEET 6 B 6 GLU B 40 GLU B 46 -1 N ASP B 42 O ASP B 53 LINK C GLU A 11 N MSE A 12 1555 1555 1.32 LINK C MSE A 12 N GLU A 13 1555 1555 1.33 LINK C GLU B 11 N MSE B 12 1555 1555 1.34 LINK C MSE B 12 N GLU B 13 1555 1555 1.34 CISPEP 1 ARG A 38 SER A 39 0 5.02 CISPEP 2 ARG B 38 SER B 39 0 -4.64 CRYST1 78.810 78.810 60.020 90.00 90.00 120.00 P 63 12 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 0.012689 0.007326 0.000000 0.00000 SCALE2 0.000000 0.014652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016661 0.00000