PDB Short entry for 2QBY HEADER REPLICATION/DNA 18-JUN-07 2QBY TITLE CRYSTAL STRUCTURE OF A HETERODIMER OF CDC6/ORC1 INITIATORS BOUND TO TITLE 2 ORIGIN DNA (FROM S. SOLFATARICUS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (33-MER); COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (33-MER); COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: CELL DIVISION CONTROL PROTEIN 6 HOMOLOG 1; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: RESIDUES 15-397; COMPND 13 SYNONYM: CDC6 HOMOLOG 1; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: CELL DIVISION CONTROL PROTEIN 6 HOMOLOG 3; COMPND 17 CHAIN: B; COMPND 18 FRAGMENT: RESIDUES 14-394; COMPND 19 SYNONYM: CDC6 HOMOLOG 3; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 7 ORGANISM_TAXID: 2287; SOURCE 8 GENE: CDC6-1; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON+; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PSV271; SOURCE 14 MOL_ID: 4; SOURCE 15 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 16 ORGANISM_TAXID: 2287; SOURCE 17 GENE: CDC6-3; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON+; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PSV271 KEYWDS WINGED-HELIX DOMAIN, HELIX-TURN-HELIX, AAA+ ATPASE DOMAIN, PROTEIN- KEYWDS 2 DNA COMPLEX, DOUBLE HELIX, REPLICATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.L.CUNNINGHAM DUEBER,J.E.CORN,S.D.BELL,J.M.BERGER REVDAT 3 30-AUG-23 2QBY 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2QBY 1 VERSN REVDAT 1 11-SEP-07 2QBY 0 JRNL AUTH E.L.DUEBER,J.E.CORN,S.D.BELL,J.M.BERGER JRNL TITL REPLICATION ORIGIN RECOGNITION AND DEFORMATION BY A JRNL TITL 2 HETERODIMERIC ARCHAEAL ORC1 COMPLEX. JRNL REF SCIENCE V. 317 1210 2007 JRNL REFN ISSN 0036-8075 JRNL PMID 17761879 JRNL DOI 10.1126/SCIENCE.1143690 REMARK 2 REMARK 2 RESOLUTION. 3.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 22548 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1215 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 3.4800 - 3.3500 0.99 0 148 0.3705 0.4376 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL 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) : 119.0 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 : 0.005 NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: THE AUTHORS STATE THAT THE ANISOU LINES REMARK 3 IN THE PDB REFER TO TLS PARAMETERS, NOT ANISOTROPIC B FACTORS. REMARK 4 REMARK 4 2QBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000043406. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11111, 0.979578, 0.979733, REMARK 200 0.987379 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24287 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.83500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.930 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: PDB ENTRY 1FNN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25MM HEPES PH 7.5, 50MM SODIUM REMARK 280 CHLORIDE, 5% GLYCEROL, 0.5MM TCEP, 15MM SPERMIDINE, 15MM SODIUM REMARK 280 CACODYLATE PH 5.0, 4.4% (W/V) PEG 3350 AND 25MM POTASSIUM REMARK 280 THIOCYANATE, MICROBATCH, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 106.70250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 106.70250 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.82450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 99.57150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.82450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 99.57150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 106.70250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.82450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 99.57150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 106.70250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.82450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 99.57150 REMARK 290 SMTRY3 8 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 300 REMARK: HETERODIMER OF ORC1-1 AND ORC1-3 BOUND TO A 33BP DNA PER REMARK 300 ASYMMETRIC UNIT 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11600 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 12 REMARK 465 ALA A 13 REMARK 465 MET A 14 REMARK 465 SER A 15 REMARK 465 SER A 16 REMARK 465 LYS A 172 REMARK 465 SER A 173 REMARK 465 SER A 311 REMARK 465 GLU A 312 REMARK 465 GLU A 313 REMARK 465 ASN A 314 REMARK 465 VAL A 315 REMARK 465 SER A 390 REMARK 465 ARG A 391 REMARK 465 PHE A 392 REMARK 465 ALA A 393 REMARK 465 ASP A 394 REMARK 465 LEU A 395 REMARK 465 TRP A 396 REMARK 465 SER A 397 REMARK 465 GLY B 11 REMARK 465 ALA B 12 REMARK 465 MET B 13 REMARK 465 GLU B 14 REMARK 465 VAL B 15 REMARK 465 ILE B 16 REMARK 465 ILE B 385 REMARK 465 GLY B 386 REMARK 465 ASP B 387 REMARK 465 PHE B 388 REMARK 465 ASP B 389 REMARK 465 ASP B 390 REMARK 465 VAL B 391 REMARK 465 GLY B 392 REMARK 465 GLU B 393 REMARK 465 ASN B 394 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DA C 1 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG C 2 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DA C 3 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT C 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA C 9 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DA C 9 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 DA C 9 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG C 10 C1' - O4' - C4' ANGL. DEV. = -10.6 DEGREES REMARK 500 DG C 13 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA C 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA C 15 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT C 19 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT C 19 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG C 21 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA C 23 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT C 26 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT C 26 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT C 28 N3 - C4 - O4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT C 33 C4' - C3' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 DT D 3 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA D 13 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DA D 13 C3' - C2' - C1' ANGL. DEV. = -7.5 DEGREES REMARK 500 DA D 13 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT D 18 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA D 20 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA D 25 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT D 29 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC D 30 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DA D 32 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA D 32 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 DG D 33 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 PRO A 30 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 PRO A 34 C - N - CA ANGL. DEV. = 11.2 DEGREES 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 ASN A 20 104.48 -163.86 REMARK 500 PRO A 26 24.79 -71.04 REMARK 500 ASP A 27 -65.33 -102.49 REMARK 500 TYR A 28 143.23 -36.94 REMARK 500 HIS A 35 -4.27 79.80 REMARK 500 ILE A 46 48.66 -103.98 REMARK 500 LEU A 47 -11.03 -163.53 REMARK 500 GLU A 53 68.30 60.14 REMARK 500 PRO A 56 -171.95 -69.27 REMARK 500 LEU A 64 -165.64 -58.96 REMARK 500 LEU A 85 -10.83 60.46 REMARK 500 PHE A 88 122.60 167.30 REMARK 500 THR A 100 122.78 -172.81 REMARK 500 ILE A 123 -67.95 -8.23 REMARK 500 LYS A 153 -89.48 -56.68 REMARK 500 LYS A 154 40.96 -88.55 REMARK 500 THR A 181 -166.26 -126.70 REMARK 500 LEU A 190 55.03 -90.06 REMARK 500 PRO A 192 -162.21 -68.13 REMARK 500 ARG A 193 -1.48 -59.96 REMARK 500 LYS A 226 -135.85 -117.32 REMARK 500 PRO A 227 -125.24 -65.31 REMARK 500 GLU A 245 59.98 -111.21 REMARK 500 HIS A 246 44.01 74.48 REMARK 500 MET A 266 33.55 -87.90 REMARK 500 LYS A 267 66.83 18.05 REMARK 500 THR A 269 47.80 -102.29 REMARK 500 ARG A 285 -51.56 -29.08 REMARK 500 PHE A 297 -38.03 -39.35 REMARK 500 ALA A 337 -147.65 -69.91 REMARK 500 GLU A 387 -19.08 -49.47 REMARK 500 ASN B 18 55.97 -142.69 REMARK 500 LYS B 20 -34.09 -167.85 REMARK 500 PHE B 34 19.09 82.47 REMARK 500 ASP B 86 -78.03 -50.58 REMARK 500 GLU B 87 -32.47 114.21 REMARK 500 LYS B 90 103.12 -48.19 REMARK 500 ASP B 91 0.00 132.82 REMARK 500 CYS B 99 -30.11 -38.80 REMARK 500 THR B 118 -74.36 -60.53 REMARK 500 PHE B 120 4.53 179.36 REMARK 500 GLU B 131 23.94 -69.77 REMARK 500 ASN B 142 112.46 3.23 REMARK 500 ILE B 143 124.59 153.51 REMARK 500 VAL B 152 -4.78 -57.66 REMARK 500 LEU B 168 -76.28 -84.99 REMARK 500 ARG B 170 33.29 -95.45 REMARK 500 SER B 171 -166.25 -101.66 REMARK 500 ALA B 173 101.11 -40.89 REMARK 500 ASN B 174 92.60 -42.69 REMARK 500 REMARK 500 THIS ENTRY HAS 66 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS B 243 GLU B 244 -147.07 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 MG A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPD C 34 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPD C 35 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 9 DBREF 2QBY A 15 397 UNP Q980N4 CDC61_SULSO 15 397 DBREF 2QBY B 14 394 UNP Q97WM8 CDC63_SULSO 14 394 DBREF 2QBY C 1 33 PDB 2QBY 2QBY 1 33 DBREF 2QBY D 1 33 PDB 2QBY 2QBY 1 33 SEQADV 2QBY GLY A 12 UNP Q980N4 EXPRESSION TAG SEQADV 2QBY ALA A 13 UNP Q980N4 EXPRESSION TAG SEQADV 2QBY MET A 14 UNP Q980N4 EXPRESSION TAG SEQADV 2QBY GLY B 11 UNP Q97WM8 EXPRESSION TAG SEQADV 2QBY ALA B 12 UNP Q97WM8 EXPRESSION TAG SEQADV 2QBY MET B 13 UNP Q97WM8 EXPRESSION TAG SEQRES 1 C 33 DA DG DA DT DT DT DT DC DA DG DA DT DG SEQRES 2 C 33 DA DA DA DC DG DT DA DG DG DA DA DA DT SEQRES 3 C 33 DT DT DA DC DA DC DT SEQRES 1 D 33 DT DG DT DA DA DA DT DT DT DC DC DT DA SEQRES 2 D 33 DC DG DT DT DT DC DA DT DC DT DG DA DA SEQRES 3 D 33 DA DA DT DC DT DA DG SEQRES 1 A 386 GLY ALA MET SER SER ILE PHE ILE ASN ARG GLU TYR LEU SEQRES 2 A 386 LEU PRO ASP TYR ILE PRO ASP GLU LEU PRO HIS ARG GLU SEQRES 3 A 386 ASP GLN ILE ARG LYS ILE ALA SER ILE LEU ALA PRO LEU SEQRES 4 A 386 TYR ARG GLU GLU LYS PRO ASN ASN ILE PHE ILE TYR GLY SEQRES 5 A 386 LEU THR GLY THR GLY LYS THR ALA VAL VAL LYS PHE VAL SEQRES 6 A 386 LEU SER LYS LEU HIS LYS LYS PHE LEU GLY LYS PHE LYS SEQRES 7 A 386 HIS VAL TYR ILE ASN THR ARG GLN ILE ASP THR PRO TYR SEQRES 8 A 386 ARG VAL LEU ALA ASP LEU LEU GLU SER LEU ASP VAL LYS SEQRES 9 A 386 VAL PRO PHE THR GLY LEU SER ILE ALA GLU LEU TYR ARG SEQRES 10 A 386 ARG LEU VAL LYS ALA VAL ARG ASP TYR GLY SER GLN VAL SEQRES 11 A 386 VAL ILE VAL LEU ASP GLU ILE ASP ALA PHE VAL LYS LYS SEQRES 12 A 386 TYR ASN ASP ASP ILE LEU TYR LYS LEU SER ARG ILE ASN SEQRES 13 A 386 SER GLU VAL ASN LYS SER LYS ILE SER PHE ILE GLY ILE SEQRES 14 A 386 THR ASN ASP VAL LYS PHE VAL ASP LEU LEU ASP PRO ARG SEQRES 15 A 386 VAL LYS SER SER LEU SER GLU GLU GLU ILE ILE PHE PRO SEQRES 16 A 386 PRO TYR ASN ALA GLU GLU LEU GLU ASP ILE LEU THR LYS SEQRES 17 A 386 ARG ALA GLN MET ALA PHE LYS PRO GLY VAL LEU PRO ASP SEQRES 18 A 386 ASN VAL ILE LYS LEU CYS ALA ALA LEU ALA ALA ARG GLU SEQRES 19 A 386 HIS GLY ASP ALA ARG ARG ALA LEU ASP LEU LEU ARG VAL SEQRES 20 A 386 SER GLY GLU ILE ALA GLU ARG MET LYS ASP THR LYS VAL SEQRES 21 A 386 LYS GLU GLU TYR VAL TYR MET ALA LYS GLU GLU ILE GLU SEQRES 22 A 386 ARG ASP ARG VAL ARG ASP ILE ILE LEU THR LEU PRO PHE SEQRES 23 A 386 HIS SER LYS LEU VAL LEU MET ALA VAL VAL SER ILE SER SEQRES 24 A 386 SER GLU GLU ASN VAL VAL SER THR THR GLY ALA VAL TYR SEQRES 25 A 386 GLU THR TYR LEU ASN ILE CYS LYS LYS LEU GLY VAL GLU SEQRES 26 A 386 ALA VAL THR GLN ARG ARG VAL SER ASP ILE ILE ASN GLU SEQRES 27 A 386 LEU ASP MET VAL GLY ILE LEU THR ALA LYS VAL VAL ASN SEQRES 28 A 386 ARG GLY ARG TYR GLY LYS THR LYS GLU ILE GLY LEU ALA SEQRES 29 A 386 VAL ASP LYS ASN ILE ILE VAL ARG SER LEU ILE GLU SER SEQRES 30 A 386 ASP SER ARG PHE ALA ASP LEU TRP SER SEQRES 1 B 384 GLY ALA MET GLU VAL ILE LYS ASN PRO LYS VAL PHE ILE SEQRES 2 B 384 ASP PRO LEU SER VAL PHE LYS GLU ILE PRO PHE ARG GLU SEQRES 3 B 384 ASP ILE LEU ARG ASP ALA ALA ILE ALA ILE ARG TYR PHE SEQRES 4 B 384 VAL LYS ASN GLU VAL LYS PHE SER ASN LEU PHE LEU GLY SEQRES 5 B 384 LEU THR GLY THR GLY LYS THR PHE VAL SER LYS TYR ILE SEQRES 6 B 384 PHE ASN GLU ILE GLU GLU VAL LYS LYS GLU ASP GLU GLU SEQRES 7 B 384 TYR LYS ASP VAL LYS GLN ALA TYR VAL ASN CYS ARG GLU SEQRES 8 B 384 VAL GLY GLY THR PRO GLN ALA VAL LEU SER SER LEU ALA SEQRES 9 B 384 GLY LYS LEU THR GLY PHE SER VAL PRO LYS HIS GLY ILE SEQRES 10 B 384 ASN LEU GLY GLU TYR ILE ASP LYS ILE LYS ASN GLY THR SEQRES 11 B 384 ARG ASN ILE ARG ALA ILE ILE TYR LEU ASP GLU VAL ASP SEQRES 12 B 384 THR LEU VAL LYS ARG ARG GLY GLY ASP ILE VAL LEU TYR SEQRES 13 B 384 GLN LEU LEU ARG SER ASP ALA ASN ILE SER VAL ILE MET SEQRES 14 B 384 ILE SER ASN ASP ILE ASN VAL ARG ASP TYR MET GLU PRO SEQRES 15 B 384 ARG VAL LEU SER SER LEU GLY PRO SER VAL ILE PHE LYS SEQRES 16 B 384 PRO TYR ASP ALA GLU GLN LEU LYS PHE ILE LEU SER LYS SEQRES 17 B 384 TYR ALA GLU TYR GLY LEU ILE LYS GLY THR TYR ASP ASP SEQRES 18 B 384 GLU ILE LEU SER TYR ILE ALA ALA ILE SER ALA LYS GLU SEQRES 19 B 384 HIS GLY ASP ALA ARG LYS ALA VAL ASN LEU LEU PHE ARG SEQRES 20 B 384 ALA ALA GLN LEU ALA SER GLY GLY GLY ILE ILE ARG LYS SEQRES 21 B 384 GLU HIS VAL ASP LYS ALA ILE VAL ASP TYR GLU GLN GLU SEQRES 22 B 384 ARG LEU ILE GLU ALA VAL LYS ALA LEU PRO PHE HIS TYR SEQRES 23 B 384 LYS LEU ALA LEU ARG SER LEU ILE GLU SER GLU ASP VAL SEQRES 24 B 384 MET SER ALA HIS LYS MET TYR THR ASP LEU CYS ASN LYS SEQRES 25 B 384 PHE LYS GLN LYS PRO LEU SER TYR ARG ARG PHE SER ASP SEQRES 26 B 384 ILE ILE SER GLU LEU ASP MET PHE GLY ILE VAL LYS ILE SEQRES 27 B 384 ARG ILE ILE ASN ARG GLY ARG ALA GLY GLY VAL LYS LYS SEQRES 28 B 384 TYR ALA LEU VAL GLU ASP LYS GLU LYS VAL LEU ARG ALA SEQRES 29 B 384 LEU ASN GLU THR PHE GLU ASP SER ILE SER ILE GLY ASP SEQRES 30 B 384 PHE ASP ASP VAL GLY GLU ASN HET SPD C 34 10 HET SPD C 35 10 HET K D 35 1 HET MG A 6 1 HET ADP A 8 27 HET MG B 7 1 HET ADP B 9 27 HETNAM SPD SPERMIDINE HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 5 SPD 2(C7 H19 N3) FORMUL 7 K K 1+ FORMUL 8 MG 2(MG 2+) FORMUL 9 ADP 2(C10 H15 N5 O10 P2) FORMUL 12 HOH *4(H2 O) HELIX 1 1 ASN A 20 LEU A 25 5 6 HELIX 2 2 ARG A 36 ILE A 46 1 11 HELIX 3 3 LEU A 47 GLU A 53 5 7 HELIX 4 4 GLY A 68 PHE A 84 1 17 HELIX 5 5 THR A 95 ASP A 99 1 5 HELIX 6 6 THR A 100 LEU A 109 1 10 HELIX 7 7 SER A 122 ASP A 136 1 15 HELIX 8 8 GLU A 147 LYS A 154 1 8 HELIX 9 9 ASP A 158 GLU A 169 1 12 HELIX 10 10 ASP A 183 LEU A 190 5 8 HELIX 11 11 PRO A 192 SER A 197 1 6 HELIX 12 12 ASN A 209 PHE A 225 1 17 HELIX 13 13 PRO A 231 GLU A 245 1 15 HELIX 14 14 ASP A 248 MET A 266 1 19 HELIX 15 15 LYS A 272 THR A 294 1 23 HELIX 16 16 PRO A 296 SER A 310 1 15 HELIX 17 17 THR A 319 GLY A 334 1 16 HELIX 18 18 THR A 339 VAL A 353 1 15 HELIX 19 19 LYS A 378 ASP A 389 1 12 HELIX 20 20 ASP B 24 PHE B 29 1 6 HELIX 21 21 ARG B 35 LYS B 51 1 17 HELIX 22 22 GLY B 67 ASP B 86 1 20 HELIX 23 23 CYS B 99 GLY B 103 1 5 HELIX 24 24 THR B 105 GLY B 119 1 15 HELIX 25 25 LEU B 129 ARG B 141 1 13 HELIX 26 26 VAL B 152 ARG B 158 1 7 HELIX 27 27 GLY B 161 ARG B 170 1 10 HELIX 28 28 GLU B 191 SER B 197 1 7 HELIX 29 29 ASP B 208 GLY B 223 1 16 HELIX 30 30 ASP B 231 LYS B 243 1 13 HELIX 31 31 ASP B 247 ALA B 262 1 16 HELIX 32 32 ARG B 269 ALA B 291 1 23 HELIX 33 33 PRO B 293 GLU B 305 1 13 HELIX 34 34 ASP B 308 PHE B 323 1 16 HELIX 35 35 SER B 329 PHE B 343 1 15 HELIX 36 36 LYS B 368 SER B 382 1 15 SHEET 1 A 5 LYS A 89 ASN A 94 0 SHEET 2 A 5 VAL A 141 ASP A 146 1 O VAL A 144 N VAL A 91 SHEET 3 A 5 ILE A 175 THR A 181 1 O SER A 176 N ILE A 143 SHEET 4 A 5 ILE A 59 GLY A 63 1 N ILE A 61 O GLY A 179 SHEET 5 A 5 GLU A 201 PHE A 205 1 O GLU A 201 N PHE A 60 SHEET 1 B 3 SER A 317 THR A 318 0 SHEET 2 B 3 LYS A 370 LEU A 374 -1 O ILE A 372 N SER A 317 SHEET 3 B 3 LEU A 356 VAL A 360 -1 N THR A 357 O GLY A 373 SHEET 1 C 5 LYS B 93 ASN B 98 0 SHEET 2 C 5 ALA B 145 ASP B 150 1 O ILE B 146 N LYS B 93 SHEET 3 C 5 ILE B 175 ILE B 180 1 O ILE B 178 N ILE B 147 SHEET 4 C 5 SER B 57 GLY B 62 1 N ASN B 58 O MET B 179 SHEET 5 C 5 SER B 201 PHE B 204 1 O PHE B 204 N LEU B 61 SHEET 1 D 2 VAL B 346 ILE B 351 0 SHEET 2 D 2 LYS B 360 VAL B 365 -1 O TYR B 362 N ARG B 349 LINK MG MG A 6 OG1 THR A 70 1555 1555 2.34 LINK MG MG B 7 O1B ADP B 9 1555 1555 2.49 CISPEP 1 GLY B 265 GLY B 266 0 2.78 SITE 1 AC1 5 HOH A 3 HOH A 4 ADP A 8 THR A 70 SITE 2 AC1 5 ASP A 146 SITE 1 AC2 5 HOH B 1 ADP B 9 THR B 69 ASP B 150 SITE 2 AC2 5 ASN B 182 SITE 1 AC3 6 DA C 20 DG C 21 DG C 22 DT D 12 SITE 2 AC3 6 DA D 13 DC D 14 SITE 1 AC4 3 DT C 26 DT C 27 DC D 30 SITE 1 AC5 17 HOH A 3 MG A 6 PRO A 26 LEU A 33 SITE 2 AC5 17 PRO A 34 THR A 65 GLY A 66 THR A 67 SITE 3 AC5 17 GLY A 68 LYS A 69 THR A 70 ALA A 71 SITE 4 AC5 17 TYR A 208 ILE A 216 ARG A 220 ALA A 249 SITE 5 AC5 17 ARG A 250 SITE 1 AC6 17 HOH B 2 MG B 7 PRO B 25 PHE B 29 SITE 2 AC6 17 ILE B 32 PRO B 33 LEU B 63 GLY B 65 SITE 3 AC6 17 THR B 66 GLY B 67 LYS B 68 THR B 69 SITE 4 AC6 17 PHE B 70 TYR B 207 TYR B 219 ALA B 248 SITE 5 AC6 17 ARG B 249 CRYST1 77.649 199.143 213.405 90.00 90.00 90.00 C 2 2 21 8 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 0.012878 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004686 0.00000