PDB Short entry for 2V1U HEADER REPLICATION 30-MAY-07 2V1U TITLE STRUCTURE OF THE AEROPYRUM PERNIX ORC1 PROTEIN IN COMPLEX TITLE 2 WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION CONTROL PROTEIN 6 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CDC6 HOMOLOG, ORC1; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*TP*CP*TP*CP*CP*AP*CP*AP*GP*GP COMPND 7 *AP*AP*AP*CP*GP*GP*AP*GP*GP*GP*GP*T)-3'; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: 22BP ORB4 ELEMENT; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*AP*CP*CP*CP*CP*TP*CP*CP*GP*TP COMPND 12 *TP*TP*CP*CP*TP*GP*TP*GP*GP*AP*GP*A)-3'; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: 22BP ORB4 ELEMENT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 56636; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 7 ORGANISM_TAXID: 56636; SOURCE 8 MOL_ID: 3; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 11 ORGANISM_TAXID: 56636 KEYWDS DNA REPLICATION, NUCLEOTIDE-BINDING, REPLICATION, ARCHAEA, KEYWDS 2 ATP-BINDING, PHOSPHORYLATION, DNA REPLICATION INITIATION EXPDTA X-RAY DIFFRACTION AUTHOR M.GAUDIER,B.S.SCHUWIRTH,S.L.WESTCOTT,D.B.WIGLEY REVDAT 4 13-JUL-11 2V1U 1 VERSN REVDAT 3 24-FEB-09 2V1U 1 VERSN REVDAT 2 09-OCT-07 2V1U 1 DBREF REVDAT 1 18-SEP-07 2V1U 0 JRNL AUTH M.GAUDIER,B.S.SCHUWIRTH,S.L.WESTCOTT,D.B.WIGLEY JRNL TITL STRUCTURAL BASIS OF DNA REPLICATION ORIGIN RECOGNITION BY JRNL TITL 2 AN ORC PROTEIN. JRNL REF SCIENCE V. 317 1213 2007 JRNL REFN ISSN 0036-8075 JRNL PMID 17761880 JRNL DOI 10.1126/SCIENCE.1143664 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 12348 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 636 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 868 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3680 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.4570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3019 REMARK 3 NUCLEIC ACID ATOMS : 896 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 102.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.07000 REMARK 3 B22 (A**2) : 5.07000 REMARK 3 B33 (A**2) : -7.61000 REMARK 3 B12 (A**2) : 2.54000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.531 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.515 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 63.427 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4096 ; 0.003 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5737 ; 1.147 ; 2.280 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 380 ;12.510 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;34.333 ;21.095 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 554 ;27.545 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;24.347 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 664 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2760 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2268 ; 0.357 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2621 ; 0.339 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 207 ; 0.285 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 31 ; 0.232 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.285 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1927 ; 2.515 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3078 ; 3.893 ; 5.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2710 ;12.113 ;20.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2659 ;14.822 ;20.000 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 37 A 211 REMARK 3 ORIGIN FOR THE GROUP (A): -16.4470 -30.3780 -27.9590 REMARK 3 T TENSOR REMARK 3 T11: 0.6351 T22: -0.3849 REMARK 3 T33: 0.0985 T12: 0.2851 REMARK 3 T13: -0.1588 T23: -0.1101 REMARK 3 L TENSOR REMARK 3 L11: 6.3184 L22: 1.9018 REMARK 3 L33: 1.9075 L12: 3.1240 REMARK 3 L13: -0.2857 L23: -0.9639 REMARK 3 S TENSOR REMARK 3 S11: 0.1065 S12: -0.0241 S13: -0.6462 REMARK 3 S21: 0.3369 S22: -0.0234 S23: -0.2100 REMARK 3 S31: 1.1832 S32: -0.0353 S33: -0.0831 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 13 A 36 REMARK 3 RESIDUE RANGE : A 212 A 278 REMARK 3 ORIGIN FOR THE GROUP (A): -7.7490 -3.6120 -17.4130 REMARK 3 T TENSOR REMARK 3 T11: -0.0488 T22: -0.5336 REMARK 3 T33: -0.3356 T12: -0.0188 REMARK 3 T13: -0.0170 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 5.3309 L22: 8.2622 REMARK 3 L33: 9.7400 L12: -4.0071 REMARK 3 L13: -1.5473 L23: 1.3854 REMARK 3 S TENSOR REMARK 3 S11: 0.6358 S12: -0.1611 S13: 0.4330 REMARK 3 S21: 0.8094 S22: -0.3226 S23: -0.4301 REMARK 3 S31: -0.1127 S32: 0.9461 S33: -0.3132 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 279 A 399 REMARK 3 ORIGIN FOR THE GROUP (A): -31.1940 -14.9770 2.5450 REMARK 3 T TENSOR REMARK 3 T11: 0.1533 T22: -0.4560 REMARK 3 T33: -0.2982 T12: -0.0768 REMARK 3 T13: -0.0191 T23: -0.1201 REMARK 3 L TENSOR REMARK 3 L11: 3.1967 L22: 5.2492 REMARK 3 L33: 3.0063 L12: 3.2697 REMARK 3 L13: -1.0744 L23: -1.8406 REMARK 3 S TENSOR REMARK 3 S11: 0.2316 S12: -0.1397 S13: 0.2499 REMARK 3 S21: 0.4434 S22: 0.0604 S23: 0.2276 REMARK 3 S31: -0.0884 S32: -0.2828 S33: -0.2920 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 22 REMARK 3 RESIDUE RANGE : C 1 C 22 REMARK 3 ORIGIN FOR THE GROUP (A): -35.4460 -35.7600 -3.1470 REMARK 3 T TENSOR REMARK 3 T11: 0.2581 T22: -0.3927 REMARK 3 T33: -0.2173 T12: -0.1884 REMARK 3 T13: -0.2227 T23: 0.0645 REMARK 3 L TENSOR REMARK 3 L11: 1.7938 L22: 1.7228 REMARK 3 L33: 5.7436 L12: 0.0521 REMARK 3 L13: 0.8016 L23: 0.6527 REMARK 3 S TENSOR REMARK 3 S11: 0.3773 S12: -0.0337 S13: -0.5631 REMARK 3 S21: -0.0304 S22: -0.0607 S23: 0.1842 REMARK 3 S31: 0.2179 S32: -0.6006 S33: -0.3166 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2V1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAY-07. REMARK 100 THE PDBE ID CODE IS EBI-32523. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97295 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12348 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.10 REMARK 200 RESOLUTION RANGE LOW (A) : 15.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.41 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.1 REMARK 200 R MERGE FOR SHELL (I) : 0.25 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.52 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: PHASER, AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 263.40667 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 131.70333 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 197.55500 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 65.85167 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 329.25833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 263.40667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 131.70333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 65.85167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 197.55500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 329.25833 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: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 AVERAGE BURIED SURFACE AREA: 1820 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 HOH A2001 LIES ON A SPECIAL POSITION. 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 175 REMARK 465 ASP A 176 REMARK 465 ARG A 177 REMARK 465 VAL A 178 REMARK 465 TRP A 179 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 O SER A 15 O PHE A 18 2.19 REMARK 500 O VAL A 23 NH1 ARG A 225 2.11 REMARK 500 O PRO A 49 CA GLY A 53 2.05 REMARK 500 N ASN A 58 OE1 GLU A 205 1.95 REMARK 500 OD1 ASN A 58 N LEU A 182 2.09 REMARK 500 NH1 ARG A 106 OP2 DC C 7 2.04 REMARK 500 OH TYR A 130 CD1 ILE A 170 2.05 REMARK 500 CG ASP A 152 OG1 THR A 186 2.06 REMARK 500 OD1 ASP A 152 OG1 THR A 186 1.90 REMARK 500 OD1 ASP A 152 CB THR A 186 1.97 REMARK 500 OD2 ASP A 152 OG1 THR A 186 2.18 REMARK 500 OD1 ASN A 171 N VAL A 180 2.04 REMARK 500 O GLN A 172 N LEU A 174 2.15 REMARK 500 CB LEU A 195 CG LYS A 200 2.00 REMARK 500 OD1 ASP A 236 CZ ARG A 275 2.10 REMARK 500 OD1 ASP A 236 NH1 ARG A 275 2.14 REMARK 500 NE ARG A 298 OE1 GLU A 391 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 B 6 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 9 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG B 9 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA B 13 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT C 10 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DT C 10 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT C 15 N3 - C4 - O4 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT C 17 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA C 22 O4' - C1' - N9 ANGL. DEV. = 2.8 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 LYS A 16 -43.03 21.39 REMARK 500 PRO A 26 6.42 -68.53 REMARK 500 TYR A 28 108.79 -49.66 REMARK 500 HIS A 35 -6.65 78.65 REMARK 500 ARG A 52 -90.79 -86.82 REMARK 500 GLU A 54 -144.62 -162.17 REMARK 500 LYS A 55 114.55 -39.20 REMARK 500 VAL A 91 89.42 -151.52 REMARK 500 TYR A 105 -73.25 -43.91 REMARK 500 SER A 109 -37.78 -39.30 REMARK 500 VAL A 126 -39.09 -30.56 REMARK 500 GLU A 150 53.24 76.49 REMARK 500 LEU A 154 -74.34 -27.58 REMARK 500 LEU A 164 -62.56 -22.79 REMARK 500 GLU A 173 47.81 -56.11 REMARK 500 SER A 188 110.99 -170.34 REMARK 500 PHE A 191 -26.97 -142.36 REMARK 500 VAL A 192 -4.29 -48.92 REMARK 500 ASN A 194 23.24 -78.20 REMARK 500 LEU A 203 -9.10 -56.25 REMARK 500 PRO A 212 -165.08 -73.52 REMARK 500 ARG A 219 -68.25 -29.33 REMARK 500 PRO A 232 49.62 -90.93 REMARK 500 ASP A 238 -10.06 85.02 REMARK 500 ARG A 249 -3.04 -56.77 REMARK 500 GLU A 250 -98.65 -138.10 REMARK 500 ARG A 271 21.41 -73.80 REMARK 500 ARG A 272 47.23 36.83 REMARK 500 GLU A 274 41.69 -86.64 REMARK 500 PRO A 301 151.27 -46.57 REMARK 500 GLU A 315 4.47 -65.07 REMARK 500 ARG A 319 83.70 -38.45 REMARK 500 PRO A 320 150.56 -49.79 REMARK 500 GLU A 340 155.86 -32.30 REMARK 500 LEU A 357 -8.25 -50.53 REMARK 500 GLU A 386 -73.35 -48.91 REMARK 500 PHE A 394 -62.60 -91.04 REMARK 500 LEU A 398 24.28 -69.59 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 SER A 15 LYS A 16 112.91 REMARK 500 ARG A 52 GLY A 53 112.14 REMARK 500 GLY A 53 GLU A 54 147.37 REMARK 500 GLU A 54 LYS A 55 -132.58 REMARK 500 ARG A 101 GLU A 102 -128.87 REMARK 500 PHE A 121 THR A 122 139.00 REMARK 500 GLY A 123 LEU A 124 -122.15 REMARK 500 LEU A 140 ARG A 141 -126.25 REMARK 500 ASN A 194 LEU A 195 143.98 REMARK 500 LEU A 195 GLU A 196 143.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ILE A 17 15.6 L L OUTSIDE RANGE REMARK 500 LEU A 140 24.3 L L OUTSIDE RANGE REMARK 500 GLN A 172 24.4 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 70 OG1 REMARK 620 2 ADP A1400 O3B 55.3 REMARK 620 3 ADP A1400 O1B 111.5 57.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1401 DBREF 2V1U A 13 399 UNP Q9YEV6 CDC6_AERPE 9 395 DBREF 2V1U B 1 22 PDB 2V1U 2V1U 1 22 DBREF 2V1U C 1 22 PDB 2V1U 2V1U 1 22 SEQRES 1 A 387 LEU GLU SER LYS ILE PHE ARG LYS ARG TRP VAL LEU LEU SEQRES 2 A 387 PRO ASP TYR VAL PRO ASP VAL LEU PRO HIS ARG GLU ALA SEQRES 3 A 387 GLU LEU ARG ARG LEU ALA GLU VAL LEU ALA PRO ALA LEU SEQRES 4 A 387 ARG GLY GLU LYS PRO SER ASN ALA LEU LEU TYR GLY LEU SEQRES 5 A 387 THR GLY THR GLY LYS THR ALA VAL ALA ARG LEU VAL LEU SEQRES 6 A 387 ARG ARG LEU GLU ALA ARG ALA SER SER LEU GLY VAL LEU SEQRES 7 A 387 VAL LYS PRO ILE TYR VAL ASN ALA ARG HIS ARG GLU THR SEQRES 8 A 387 PRO TYR ARG VAL ALA SER ALA ILE ALA GLU ALA VAL GLY SEQRES 9 A 387 VAL ARG VAL PRO PHE THR GLY LEU SER VAL GLY GLU VAL SEQRES 10 A 387 TYR GLU ARG LEU VAL LYS ARG LEU SER ARG LEU ARG GLY SEQRES 11 A 387 ILE TYR ILE ILE VAL LEU ASP GLU ILE ASP PHE LEU PRO SEQRES 12 A 387 LYS ARG PRO GLY GLY GLN ASP LEU LEU TYR ARG ILE THR SEQRES 13 A 387 ARG ILE ASN GLN GLU LEU GLY ASP ARG VAL TRP VAL SER SEQRES 14 A 387 LEU VAL GLY ILE THR ASN SER LEU GLY PHE VAL GLU ASN SEQRES 15 A 387 LEU GLU PRO ARG VAL LYS SER SER LEU GLY GLU VAL GLU SEQRES 16 A 387 LEU VAL PHE PRO PRO TYR THR ALA PRO GLN LEU ARG ASP SEQRES 17 A 387 ILE LEU GLU THR ARG ALA GLU GLU ALA PHE ASN PRO GLY SEQRES 18 A 387 VAL LEU ASP PRO ASP VAL VAL PRO LEU CYS ALA ALA LEU SEQRES 19 A 387 ALA ALA ARG GLU HIS GLY ASP ALA ARG ARG ALA LEU ASP SEQRES 20 A 387 LEU LEU ARG VAL ALA GLY GLU ILE ALA GLU ARG ARG ARG SEQRES 21 A 387 GLU GLU ARG VAL ARG ARG GLU HIS VAL TYR SER ALA ARG SEQRES 22 A 387 ALA GLU ILE GLU ARG ASP ARG VAL SER GLU VAL VAL ARG SEQRES 23 A 387 THR LEU PRO LEU HIS ALA LYS LEU VAL LEU LEU SER ILE SEQRES 24 A 387 MET MET LEU GLU ASP GLY GLY ARG PRO ALA SER THR GLY SEQRES 25 A 387 GLU ILE TYR GLU ARG TYR LYS GLU LEU THR SER THR LEU SEQRES 26 A 387 GLY LEU GLU HIS VAL THR LEU ARG ARG VAL SER GLY ILE SEQRES 27 A 387 ILE SER GLU LEU ASP MET LEU GLY ILE VAL LYS SER ARG SEQRES 28 A 387 VAL VAL SER ARG GLY ARG TYR GLY LYS THR ARG GLU VAL SEQRES 29 A 387 SER LEU ASP ALA ASP ARG LEU ALA VAL GLU ASN ALA LEU SEQRES 30 A 387 SER GLU ASP PRO PHE VAL ALA ARG LEU LEU SEQRES 1 B 22 DT DC DT DC DC DA DC DA DG DG DA DA DA SEQRES 2 B 22 DC DG DG DA DG DG DG DG DT SEQRES 1 C 22 DA DC DC DC DC DT DC DC DG DT DT DT DC SEQRES 2 C 22 DC DT DG DT DG DG DA DG DA HET ADP A1400 27 HET MG A1401 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 MG MG 2+ FORMUL 6 HOH *8(H2 O) HELIX 1 1 LYS A 20 LEU A 25 1 6 HELIX 2 2 ARG A 36 VAL A 46 1 11 HELIX 3 3 LEU A 47 LEU A 51 5 5 HELIX 4 4 GLY A 68 GLY A 88 1 21 HELIX 5 5 THR A 103 GLY A 116 1 14 HELIX 6 6 SER A 125 SER A 138 1 14 HELIX 7 7 ASP A 152 ARG A 157 1 6 HELIX 8 8 GLY A 159 ILE A 170 1 12 HELIX 9 9 ASN A 171 GLU A 173 5 3 HELIX 10 10 GLU A 196 SER A 201 1 6 HELIX 11 11 THR A 214 PHE A 230 1 17 HELIX 12 12 ASP A 238 ARG A 249 1 12 HELIX 13 13 ASP A 253 ARG A 271 1 19 HELIX 14 14 ARG A 277 THR A 299 1 23 HELIX 15 15 PRO A 301 GLU A 315 1 15 HELIX 16 16 THR A 323 LEU A 337 1 15 HELIX 17 17 THR A 343 LEU A 357 1 15 HELIX 18 18 GLY A 368 TYR A 370 5 3 HELIX 19 19 ASP A 381 ASP A 392 1 12 HELIX 20 20 PHE A 394 LEU A 399 5 6 SHEET 1 AA 5 VAL A 91 ASN A 97 0 SHEET 2 AA 5 ILE A 143 ASP A 149 1 O ILE A 143 N LYS A 92 SHEET 3 AA 5 SER A 181 ILE A 185 1 O SER A 181 N ILE A 146 SHEET 4 AA 5 ALA A 59 LEU A 61 1 O ALA A 59 N GLY A 184 SHEET 5 AA 5 VAL A 206 GLU A 207 1 O VAL A 206 N LEU A 60 SHEET 1 AB 3 ALA A 321 SER A 322 0 SHEET 2 AB 3 LYS A 372 LEU A 378 -1 O VAL A 376 N ALA A 321 SHEET 3 AB 3 VAL A 360 SER A 366 -1 O LYS A 361 N SER A 377 LINK MG MG A1401 OG1 THR A 70 1555 1555 2.16 LINK MG MG A1401 O3B ADP A1400 1555 1555 2.56 LINK MG MG A1401 O1B ADP A1400 1555 1555 2.66 SITE 1 AC1 15 LEU A 33 PRO A 34 GLY A 66 THR A 67 SITE 2 AC1 15 GLY A 68 LYS A 69 THR A 70 ALA A 71 SITE 3 AC1 15 TYR A 213 ILE A 221 ARG A 225 ALA A 254 SITE 4 AC1 15 ARG A 255 LEU A 258 MG A1401 SITE 1 AC2 2 THR A 70 ADP A1400 CRYST1 75.700 75.700 395.110 90.00 90.00 120.00 P 65 2 2 24 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 0.013210 0.007627 0.000000 0.00000 SCALE2 0.000000 0.015254 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002531 0.00000