PDB Short entry for 2NTC HEADER DNA BINDING PROTEIN/DNA 07-NOV-06 2NTC TITLE CRYSTAL STRUCTURE OF SV40 LARGE T ANTIGEN ORIGIN BINDING DOMAIN WITH TITLE 2 DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 21-NT PEN ELEMENT OF THE SV40 DNA ORIGIN; COMPND 3 CHAIN: W; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 21-NT PEN ELEMENT OF THE SV40 DNA ORIGIN; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LARGE T ANTIGEN; COMPND 11 CHAIN: A, B; COMPND 12 FRAGMENT: ORIGIN BINDING DOMAIN (RESIDUES 131-259); COMPND 13 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: SIMIAN VIRUS 40; SOURCE 7 ORGANISM_TAXID: 10633; SOURCE 8 STRAIN: 776; SOURCE 9 GENE: LARGE T ANTIGEN; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PGEX-1LT KEYWDS ORIGIN BINDING DOMAIN; PROTEIN-DNA COMPLEX; REPLICATION, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.BOHM,G.MEINKE,P.A.BULLOCK REVDAT 5 03-APR-24 2NTC 1 REMARK REVDAT 4 27-DEC-23 2NTC 1 SEQADV REVDAT 3 13-JUL-11 2NTC 1 VERSN REVDAT 2 24-FEB-09 2NTC 1 VERSN REVDAT 1 13-FEB-07 2NTC 0 JRNL AUTH G.MEINKE,P.PHELAN,S.MOINE,E.BOCHKAREVA,A.BOCHKAREV, JRNL AUTH 2 P.A.BULLOCK,A.BOHM JRNL TITL THE CRYSTAL STRUCTURE OF THE SV40 T-ANTIGEN ORIGIN BINDING JRNL TITL 2 DOMAIN IN COMPLEX WITH DNA JRNL REF PLOS BIOL. V. 5 E23 2007 JRNL REFN ISSN 1544-9173 JRNL PMID 17253903 JRNL DOI 10.1371/JOURNAL.PBIO.0050023 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 3 NUMBER OF REFLECTIONS : 14921 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 772 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 706 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 58.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 29 REMARK 3 BIN FREE R VALUE : 0.4130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2063 REMARK 3 NUCLEIC ACID ATOMS : 855 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 77 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) : 53.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.98000 REMARK 3 B22 (A**2) : -4.37000 REMARK 3 B33 (A**2) : 5.35000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.523 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.325 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.261 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.329 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3079 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4343 ; 2.013 ; 2.299 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 251 ; 8.012 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;34.099 ;23.200 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 361 ;19.290 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;24.621 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 480 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2041 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1239 ; 0.239 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1969 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 137 ; 0.208 ; 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): 25 ; 0.192 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.459 ; 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): 1299 ; 0.878 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2055 ; 1.575 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2295 ; 1.868 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2288 ; 2.866 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 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 233 A 258 REMARK 3 ORIGIN FOR THE GROUP (A): -9.2610 -29.1450 1.9760 REMARK 3 T TENSOR REMARK 3 T11: -0.2066 T22: 0.0503 REMARK 3 T33: 0.2779 T12: -0.0508 REMARK 3 T13: 0.0315 T23: 0.0774 REMARK 3 L TENSOR REMARK 3 L11: 8.3983 L22: 9.9159 REMARK 3 L33: 9.7363 L12: 3.3512 REMARK 3 L13: 5.6721 L23: 3.5961 REMARK 3 S TENSOR REMARK 3 S11: -0.0880 S12: -0.2650 S13: -0.9330 REMARK 3 S21: -0.1593 S22: 0.6771 S23: 0.9447 REMARK 3 S31: 1.0058 S32: -0.1001 S33: -0.5891 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 233 B 258 REMARK 3 ORIGIN FOR THE GROUP (A): 22.9650 25.5320 9.5980 REMARK 3 T TENSOR REMARK 3 T11: -0.0875 T22: 0.0495 REMARK 3 T33: 0.5437 T12: 0.0462 REMARK 3 T13: -0.1449 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 6.8670 L22: 7.2487 REMARK 3 L33: 2.1889 L12: -4.0374 REMARK 3 L13: 2.2804 L23: 1.3011 REMARK 3 S TENSOR REMARK 3 S11: -0.2292 S12: -0.5219 S13: 1.0703 REMARK 3 S21: 0.7454 S22: -0.3025 S23: -1.2936 REMARK 3 S31: -0.9327 S32: 0.1339 S33: 0.5317 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : W 2 W 21 REMARK 3 RESIDUE RANGE : C 23 C 43 REMARK 3 ORIGIN FOR THE GROUP (A): 11.7910 -2.9720 -17.8010 REMARK 3 T TENSOR REMARK 3 T11: -0.0638 T22: -0.2667 REMARK 3 T33: 0.1124 T12: -0.0026 REMARK 3 T13: 0.0385 T23: -0.0388 REMARK 3 L TENSOR REMARK 3 L11: 1.1212 L22: 10.3252 REMARK 3 L33: 0.3335 L12: -0.8682 REMARK 3 L13: 0.0260 L23: -0.0937 REMARK 3 S TENSOR REMARK 3 S11: 0.0939 S12: 0.0082 S13: -0.1424 REMARK 3 S21: -0.8168 S22: -0.1762 S23: -0.0307 REMARK 3 S31: -0.0025 S32: 0.0034 S33: 0.0823 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2NTC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15314 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : 0.10000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: T ANTIGEN ORIGIN BINDING DOMAIN AND FOUR BASE REMARK 200 PAIRS DUPLEX DNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.5, 0.1 M REMARK 280 CALCIUM ACETATE, 30 % V/V PEG 8000, 20 % GLYCEROL, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 273K 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 32.24450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.63100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.17050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.63100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.24450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.17050 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS TWO T-ANTIGEN ORIGIN BINDING REMARK 300 DOMAIN MOLECULES BOUND TO A DNA TARGET THAT CONTAINS TWO HIGH REMARK 300 AFFINITY BINDING SITES 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 APPLY THE FOLLOWING TO CHAINS: W, C, 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 129 REMARK 465 SER A 130 REMARK 465 LYS A 131 REMARK 465 PRO A 259 REMARK 465 GLU A 260 REMARK 465 SER A 261 REMARK 465 SER A 262 REMARK 465 GLY B 129 REMARK 465 SER B 130 REMARK 465 LYS B 131 REMARK 465 VAL B 132 REMARK 465 PRO B 259 REMARK 465 GLU B 260 REMARK 465 SER B 261 REMARK 465 SER B 262 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 136 CG CD CE NZ REMARK 470 LYS B 173 CG CD CE NZ 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 N7 DA C 34 O HOH C 46 1.96 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 O5' DT C 23 O3' DG C 43 1545 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT W 13 N1 DT W 13 C2 0.052 REMARK 500 DC C 40 O3' DC C 40 C3' -0.040 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 W 1 N1 - C6 - N6 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA W 1 C5 - C6 - N6 ANGL. DEV. = -6.5 DEGREES REMARK 500 DC W 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC W 2 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 DA W 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA W 4 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DG W 5 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 DG W 5 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DG W 5 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 DG W 5 N1 - C6 - O6 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG W 5 C5 - C6 - O6 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG W 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC W 9 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 DT W 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT W 10 C4 - C5 - C7 ANGL. DEV. = 7.7 DEGREES REMARK 500 DT W 10 C6 - C5 - C7 ANGL. DEV. = -6.4 DEGREES REMARK 500 DC W 12 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES REMARK 500 DT W 13 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG W 14 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG W 15 N3 - C4 - C5 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG W 15 C5 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC W 16 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC W 17 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT W 20 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT W 20 C4 - C5 - C7 ANGL. DEV. = 5.4 DEGREES REMARK 500 DT W 20 C6 - C5 - C7 ANGL. DEV. = -6.1 DEGREES REMARK 500 DG W 21 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DC C 24 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC C 24 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES REMARK 500 DA C 25 N1 - C6 - N6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA C 25 C5 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG C 28 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 DG C 28 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA C 34 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 DG C 36 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT C 37 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DT C 37 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 DT C 37 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT C 37 N3 - C4 - O4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC C 39 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT C 41 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 DG C 43 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 204 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 204 NE - CZ - NH2 ANGL. DEV. = -3.5 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 PHE A 138 160.60 -48.32 REMARK 500 TYR A 190 62.91 37.14 REMARK 500 CYS A 216 -149.42 -58.48 REMARK 500 THR A 217 -68.73 -175.10 REMARK 500 PHE A 218 -21.73 112.51 REMARK 500 ASP B 134 -89.15 -46.03 REMARK 500 ALA B 149 135.53 -31.83 REMARK 500 TYR B 190 79.65 43.54 REMARK 500 ASN B 191 -24.08 73.78 REMARK 500 HIS B 192 -156.72 -129.53 REMARK 500 THR B 217 109.01 54.53 REMARK 500 PHE B 218 40.99 -71.02 REMARK 500 LYS B 228 79.22 -116.29 REMARK 500 ASP B 256 -38.84 106.45 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 CYS B 216 THR B 217 35.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TBD RELATED DB: PDB REMARK 900 NMR OF SAME PROTEIN REMARK 900 RELATED ID: 2FUF RELATED DB: PDB REMARK 900 HIGH RESOLUTION OPEN-RING FORM OF SAME PROTEIN DBREF 2NTC A 131 260 UNP P03070 TALA_SV40 131 260 DBREF 2NTC B 131 260 UNP P03070 TALA_SV40 131 260 DBREF 2NTC W 1 21 PDB 2NTC 2NTC 1 21 DBREF 2NTC C 23 43 PDB 2NTC 2NTC 23 43 SEQADV 2NTC GLY A 129 UNP P03070 CLONING ARTIFACT SEQADV 2NTC SER A 130 UNP P03070 CLONING ARTIFACT SEQADV 2NTC SER A 261 UNP P03070 CLONING ARTIFACT SEQADV 2NTC SER A 262 UNP P03070 CLONING ARTIFACT SEQADV 2NTC GLY B 129 UNP P03070 CLONING ARTIFACT SEQADV 2NTC SER B 130 UNP P03070 CLONING ARTIFACT SEQADV 2NTC SER B 261 UNP P03070 CLONING ARTIFACT SEQADV 2NTC SER B 262 UNP P03070 CLONING ARTIFACT SEQRES 1 W 21 DA DC DG DA DG DG DC DA DC DT DT DC DT SEQRES 2 W 21 DG DG DC DC DT DC DT DG SEQRES 1 C 21 DT DC DA DG DA DG DG DC DC DA DG DA DA SEQRES 2 C 21 DG DT DG DC DC DT DC DG SEQRES 1 A 134 GLY SER LYS VAL GLU ASP PRO LYS ASP PHE PRO SER GLU SEQRES 2 A 134 LEU LEU SER PHE LEU SER HIS ALA VAL PHE SER ASN ARG SEQRES 3 A 134 THR LEU ALA CYS PHE ALA ILE TYR THR THR LYS GLU LYS SEQRES 4 A 134 ALA ALA LEU LEU TYR LYS LYS ILE MET GLU LYS TYR SER SEQRES 5 A 134 VAL THR PHE ILE SER ARG HIS ASN SER TYR ASN HIS ASN SEQRES 6 A 134 ILE LEU PHE PHE LEU THR PRO HIS ARG HIS ARG VAL SER SEQRES 7 A 134 ALA ILE ASN ASN TYR ALA GLN LYS LEU CYS THR PHE SER SEQRES 8 A 134 PHE LEU ILE CYS LYS GLY VAL ASN LYS GLU TYR LEU MET SEQRES 9 A 134 TYR SER ALA LEU THR ARG ASP PRO PHE SER VAL ILE GLU SEQRES 10 A 134 GLU SER LEU PRO GLY GLY LEU LYS GLU HIS ASP PHE ASN SEQRES 11 A 134 PRO GLU SER SER SEQRES 1 B 134 GLY SER LYS VAL GLU ASP PRO LYS ASP PHE PRO SER GLU SEQRES 2 B 134 LEU LEU SER PHE LEU SER HIS ALA VAL PHE SER ASN ARG SEQRES 3 B 134 THR LEU ALA CYS PHE ALA ILE TYR THR THR LYS GLU LYS SEQRES 4 B 134 ALA ALA LEU LEU TYR LYS LYS ILE MET GLU LYS TYR SER SEQRES 5 B 134 VAL THR PHE ILE SER ARG HIS ASN SER TYR ASN HIS ASN SEQRES 6 B 134 ILE LEU PHE PHE LEU THR PRO HIS ARG HIS ARG VAL SER SEQRES 7 B 134 ALA ILE ASN ASN TYR ALA GLN LYS LEU CYS THR PHE SER SEQRES 8 B 134 PHE LEU ILE CYS LYS GLY VAL ASN LYS GLU TYR LEU MET SEQRES 9 B 134 TYR SER ALA LEU THR ARG ASP PRO PHE SER VAL ILE GLU SEQRES 10 B 134 GLU SER LEU PRO GLY GLY LEU LYS GLU HIS ASP PHE ASN SEQRES 11 B 134 PRO GLU SER SER FORMUL 5 HOH *77(H2 O) HELIX 1 1 THR A 164 SER A 180 1 17 HELIX 2 2 ARG A 204 LYS A 214 1 11 HELIX 3 3 LYS A 228 ARG A 238 1 11 HELIX 4 4 GLY A 250 GLU A 254 5 5 HELIX 5 5 LEU B 142 LEU B 146 5 5 HELIX 6 6 THR B 164 SER B 180 1 17 HELIX 7 7 ARG B 204 LYS B 214 1 11 HELIX 8 8 LYS B 228 ARG B 238 1 11 SHEET 1 A 5 LEU A 221 GLY A 225 0 SHEET 2 A 5 LEU A 156 THR A 163 -1 N TYR A 162 O ILE A 222 SHEET 3 A 5 HIS A 192 HIS A 203 -1 O HIS A 203 N LEU A 156 SHEET 4 A 5 PHE A 183 SER A 189 -1 N SER A 189 O HIS A 192 SHEET 5 A 5 SER A 242 GLU A 246 -1 O SER A 242 N ASN A 188 SHEET 1 B 5 LEU B 221 GLY B 225 0 SHEET 2 B 5 LEU B 156 THR B 163 -1 N TYR B 162 O ILE B 222 SHEET 3 B 5 HIS B 192 HIS B 203 -1 O HIS B 203 N LEU B 156 SHEET 4 B 5 PHE B 183 SER B 189 -1 N SER B 185 O PHE B 196 SHEET 5 B 5 SER B 242 GLU B 246 -1 O GLU B 245 N ARG B 186 CISPEP 1 THR A 217 PHE A 218 0 13.32 CISPEP 2 ASP A 239 PRO A 240 0 -3.32 CISPEP 3 ASP B 239 PRO B 240 0 10.50 CRYST1 64.489 68.341 97.262 90.00 90.00 90.00 P 21 21 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 0.015507 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010282 0.00000