10 20 30 40 50 60 70 80 1IMO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LIGASE 11-MAY-01 1IMO
TITLE NMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE III; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BRCT DOMAIN; COMPND 5 SYNONYM: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP]; COMPND 6 EC: 6.5.1.1; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: BL21(DE3)
KEYWDS PARALLEL BETA SHEET, LIGASE
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR V.V.KRISHNAN,K.H.THORNTON,M.P.THELEN,M.COSMAN
REVDAT 4 24-FEB-09 1IMO 1 VERSN REVDAT 3 01-APR-03 1IMO 1 JRNL REVDAT 2 09-NOV-01 1IMO 1 JRNL REVDAT 1 25-MAY-01 1IMO 0
JRNL AUTH V.V.KRISHNAN,K.H.THORNTON,M.P.THELEN,M.COSMAN JRNL TITL SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF THE JRNL TITL 2 HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN JRNL REF BIOCHEMISTRY V. 40 13158 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11683624 JRNL DOI 10.1021/BI010979G
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.COSMAN,V.V.KRISHNAN,K.H.THORNTON,M.P.THELEN REMARK 1 TITL EXPRESSION, PURIFICATION, AND BIOPHYSICAL REMARK 1 TITL 2 CHARACTERIZATION OF THE BRCT DOMAIN OF HUMAN DNA REMARK 1 TITL 3 LIGASE III ALPHA REMARK 1 REF PROTEIN EXPR.PURIF. V. 21 401 2001 REMARK 1 REFN ISSN 1046-5928 REMARK 1 DOI 10.1006/PREP.2001.1391
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : WUTHRICH ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 1072 RESTRAINTS, 979 NOE-DERIVED DISTANCE CONSTRAINTS, 25 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 54 H BOND RESTRAINTS FROM HYDROGEN REMARK 3 BONDS
REMARK 4 REMARK 4 1IMO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-01. REMARK 100 THE RCSB ID CODE IS RCSB013413.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : 0.4-1.0 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 50 MM NAH2PO4, 150 MM NACL, REMARK 210 25 MM D10-DTTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY, 2D NOESY, REMARK 210 HNHA, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2.3, DYANA 1.5 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, TORSION ANGLE REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 299 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURE WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURE REMARK 210 WITH THE LOWEST ENERGY, TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY
REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 CG2 ILE A 850 N ILE A 913 1.52 REMARK 500 O ARG A 855 N HIS A 890 1.52 REMARK 500 CG ARG A 855 CG2 THR A 889 1.71 REMARK 500 CG2 ILE A 850 C CYS A 912 1.74 REMARK 500 CG ARG A 855 CB THR A 889 1.75 REMARK 500 O MET A 885 N ALA A 888 1.77 REMARK 500 CD ARG A 855 CB THR A 889 1.81 REMARK 500 CG2 ILE A 850 CA ILE A 913 1.98 REMARK 500 OH TYR A 871 CD1 ILE A 913 2.00 REMARK 500 O MET A 885 N SER A 887 2.01 REMARK 500 NE ARG A 855 CB THR A 889 2.01 REMARK 500 O GLN A 881 N ASP A 884 2.03 REMARK 500 O ARG A 895 N ASN A 898 2.09 REMARK 500 O SER A 894 NZ LYS A 897 2.11 REMARK 500 O ARG A 855 CA HIS A 890 2.12 REMARK 500 CD1 ILE A 850 CA ILE A 913 2.12 REMARK 500 CG2 ILE A 850 O CYS A 912 2.18 REMARK 500 CB ARG A 855 CG2 THR A 889 2.19 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 GLY A 835 N GLY A 835 CA -0.891 REMARK 500 GLY A 835 CA GLY A 835 C -0.226 REMARK 500 GLY A 835 C GLY A 835 O -0.593 REMARK 500 SER A 836 N SER A 836 CA -0.219 REMARK 500 SER A 836 CA SER A 836 CB -0.218 REMARK 500 SER A 836 CB SER A 836 OG -0.813 REMARK 500 GLY A 835 C SER A 836 N -0.464 REMARK 500 ASP A 838 CB ASP A 838 CG -0.880 REMARK 500 ASP A 838 CG ASP A 838 OD1 -0.925 REMARK 500 ASP A 838 CG ASP A 838 OD2 -0.912 REMARK 500 GLU A 839 CG GLU A 839 CD -0.173 REMARK 500 GLU A 839 CD GLU A 839 OE1 -0.714 REMARK 500 GLU A 839 CD GLU A 839 OE2 -0.720 REMARK 500 THR A 840 CB THR A 840 OG1 -0.394 REMARK 500 THR A 840 CB THR A 840 CG2 -0.344 REMARK 500 LEU A 841 CB LEU A 841 CG -0.291 REMARK 500 LEU A 841 CG LEU A 841 CD1 -0.563 REMARK 500 LEU A 841 CG LEU A 841 CD2 -0.509 REMARK 500 CYS A 842 CB CYS A 842 SG -0.454 REMARK 500 GLN A 843 CD GLN A 843 OE1 -0.361 REMARK 500 GLN A 843 CD GLN A 843 NE2 -0.358 REMARK 500 THR A 844 C THR A 844 O -0.529 REMARK 500 LYS A 845 CG LYS A 845 CD -0.457 REMARK 500 LYS A 845 CD LYS A 845 CE -0.162 REMARK 500 LYS A 845 CE LYS A 845 NZ -0.269 REMARK 500 THR A 844 C LYS A 845 N -0.246 REMARK 500 VAL A 846 CB VAL A 846 CG1 -0.341 REMARK 500 VAL A 846 CB VAL A 846 CG2 -0.466 REMARK 500 VAL A 846 C VAL A 846 O -0.697 REMARK 500 LEU A 847 C LEU A 847 O -0.795 REMARK 500 VAL A 846 C LEU A 847 N -0.510 REMARK 500 LEU A 847 C LEU A 848 N -0.546 REMARK 500 ASP A 849 CB ASP A 849 CG -0.618 REMARK 500 ASP A 849 CG ASP A 849 OD1 -0.950 REMARK 500 ASP A 849 CG ASP A 849 OD2 -0.780 REMARK 500 PHE A 851 CG PHE A 851 CD2 -0.542 REMARK 500 PHE A 851 CG PHE A 851 CD1 -0.541 REMARK 500 PHE A 851 CE1 PHE A 851 CZ -0.528 REMARK 500 PHE A 851 CZ PHE A 851 CE2 -0.526 REMARK 500 THR A 852 CB THR A 852 OG1 -0.149 REMARK 500 GLY A 853 C GLY A 853 O -0.112 REMARK 500 ARG A 855 CB ARG A 855 CG -0.374 REMARK 500 ARG A 855 CG ARG A 855 CD -0.165 REMARK 500 ARG A 855 CD ARG A 855 NE -0.282 REMARK 500 ARG A 855 NE ARG A 855 CZ -0.287 REMARK 500 ARG A 855 CZ ARG A 855 NH1 -0.760 REMARK 500 ARG A 855 CZ ARG A 855 NH2 -0.266 REMARK 500 LEU A 856 CG LEU A 856 CD2 -0.351 REMARK 500 TYR A 857 CG TYR A 857 CD2 -0.653 REMARK 500 TYR A 857 CG TYR A 857 CD1 -0.645 REMARK 500 REMARK 500 THIS ENTRY HAS 143 BOND DEVIATIONS. 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 GLY A 835 N - CA - C ANGL. DEV. = 26.7 DEGREES REMARK 500 SER A 836 CA - CB - OG ANGL. DEV. = 20.4 DEGREES REMARK 500 GLY A 835 CA - C - N ANGL. DEV. = 22.0 DEGREES REMARK 500 GLY A 835 O - C - N ANGL. DEV. = -29.7 DEGREES REMARK 500 SER A 836 C - N - CA ANGL. DEV. = 20.4 DEGREES REMARK 500 ASP A 838 CA - CB - CG ANGL. DEV. = 35.9 DEGREES REMARK 500 ASP A 838 OD1 - CG - OD2 ANGL. DEV. = -34.7 DEGREES REMARK 500 ASP A 838 CB - CG - OD1 ANGL. DEV. = 16.4 DEGREES REMARK 500 ASP A 838 CB - CG - OD2 ANGL. DEV. = 18.4 DEGREES REMARK 500 GLU A 839 OE1 - CD - OE2 ANGL. DEV. = -82.1 DEGREES REMARK 500 GLU A 839 CG - CD - OE1 ANGL. DEV. = 41.3 DEGREES REMARK 500 GLU A 839 CG - CD - OE2 ANGL. DEV. = 40.9 DEGREES REMARK 500 THR A 840 CA - CB - CG2 ANGL. DEV. = 8.8 DEGREES REMARK 500 LEU A 841 CB - CG - CD1 ANGL. DEV. = 10.8 DEGREES REMARK 500 LEU A 841 CB - CG - CD2 ANGL. DEV. = -15.7 DEGREES REMARK 500 GLN A 843 OE1 - CD - NE2 ANGL. DEV. = -23.9 DEGREES REMARK 500 LYS A 845 CB - CG - CD ANGL. DEV. = 24.5 DEGREES REMARK 500 LYS A 845 CG - CD - CE ANGL. DEV. = 34.2 DEGREES REMARK 500 THR A 844 CA - C - N ANGL. DEV. = 23.4 DEGREES REMARK 500 THR A 844 O - C - N ANGL. DEV. = -21.9 DEGREES REMARK 500 LYS A 845 C - N - CA ANGL. DEV. = 22.1 DEGREES REMARK 500 VAL A 846 CG1 - CB - CG2 ANGL. DEV. = -12.3 DEGREES REMARK 500 VAL A 846 CA - CB - CG1 ANGL. DEV. = 13.6 DEGREES REMARK 500 VAL A 846 CA - C - O ANGL. DEV. = 28.6 DEGREES REMARK 500 LEU A 847 CA - C - O ANGL. DEV. = 56.9 DEGREES REMARK 500 VAL A 846 CA - C - N ANGL. DEV. = 40.6 DEGREES REMARK 500 VAL A 846 O - C - N ANGL. DEV. = -69.1 DEGREES REMARK 500 LEU A 847 C - N - CA ANGL. DEV. = 37.5 DEGREES REMARK 500 LEU A 847 CA - C - N ANGL. DEV. = 60.9 DEGREES REMARK 500 LEU A 847 O - C - N ANGL. DEV. = -117.8 DEGREES REMARK 500 LEU A 848 C - N - CA ANGL. DEV. = 56.5 DEGREES REMARK 500 ASP A 849 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 ASP A 849 OD1 - CG - OD2 ANGL. DEV. = -62.0 DEGREES REMARK 500 ASP A 849 CB - CG - OD1 ANGL. DEV. = 23.5 DEGREES REMARK 500 ASP A 849 CB - CG - OD2 ANGL. DEV. = 38.6 DEGREES REMARK 500 PHE A 851 CB - CG - CD2 ANGL. DEV. = 25.2 DEGREES REMARK 500 PHE A 851 CD1 - CG - CD2 ANGL. DEV. = -50.6 DEGREES REMARK 500 PHE A 851 CB - CG - CD1 ANGL. DEV. = 25.5 DEGREES REMARK 500 PHE A 851 CG - CD1 - CE1 ANGL. DEV. = 25.5 DEGREES REMARK 500 PHE A 851 CG - CD2 - CE2 ANGL. DEV. = 25.2 DEGREES REMARK 500 PHE A 851 CD1 - CE1 - CZ ANGL. DEV. = 25.9 DEGREES REMARK 500 PHE A 851 CE1 - CZ - CE2 ANGL. DEV. = -52.3 DEGREES REMARK 500 PHE A 851 CZ - CE2 - CD2 ANGL. DEV. = 26.2 DEGREES REMARK 500 ARG A 855 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG A 855 CD - NE - CZ ANGL. DEV. = 26.7 DEGREES REMARK 500 ARG A 855 NH1 - CZ - NH2 ANGL. DEV. = -11.7 DEGREES REMARK 500 ARG A 855 NE - CZ - NH1 ANGL. DEV. = -16.7 DEGREES REMARK 500 ARG A 855 NE - CZ - NH2 ANGL. DEV. = 28.4 DEGREES REMARK 500 LEU A 856 CB - CG - CD1 ANGL. DEV. = 11.3 DEGREES REMARK 500 TYR A 857 CB - CG - CD2 ANGL. DEV. = 39.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 170 ANGLE DEVIATIONS. 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 THR A 840 -61.91 -99.19 REMARK 500 CYS A 842 -9.19 -55.15 REMARK 500 GLN A 843 61.16 -108.92 REMARK 500 THR A 844 -51.24 61.13 REMARK 500 LYS A 845 -5.78 -172.03 REMARK 500 VAL A 846 -126.64 37.61 REMARK 500 LEU A 847 -142.52 117.35 REMARK 500 LEU A 848 173.43 128.00 REMARK 500 ILE A 850 -92.05 -76.78 REMARK 500 PHE A 851 28.32 -59.66 REMARK 500 THR A 852 107.09 -36.84 REMARK 500 SER A 866 -67.81 -28.31 REMARK 500 ARG A 869 -85.68 -66.33 REMARK 500 PHE A 872 -90.92 -45.55 REMARK 500 VAL A 873 -35.65 -31.54 REMARK 500 ASP A 876 11.12 146.74 REMARK 500 GLU A 882 -69.38 -26.60 REMARK 500 PHE A 883 14.81 -66.20 REMARK 500 MET A 885 -39.18 -146.71 REMARK 500 THR A 886 -52.04 -5.24 REMARK 500 ALA A 888 -177.01 -46.56 REMARK 500 THR A 889 -42.01 -133.44 REMARK 500 SER A 894 172.15 85.60 REMARK 500 ARG A 895 -32.31 -141.99 REMARK 500 ASP A 896 -77.99 -13.47 REMARK 500 LYS A 897 -34.13 -31.38 REMARK 500 REMARK 500 REMARK: NULL
DBREF 1IMO A 835 922 UNP P49916 DNL3_HUMAN 835 922
SEQADV 1IMO GLY A 835 UNP P49916 LYS 835 CLONING ARTIFACT SEQADV 1IMO SER A 836 UNP P49916 ALA 836 CLONING ARTIFACT
SEQRES 1 A 88 GLY SER ALA ASP GLU THR LEU CYS GLN THR LYS VAL LEU SEQRES 2 A 88 LEU ASP ILE PHE THR GLY VAL ARG LEU TYR LEU PRO PRO SEQRES 3 A 88 SER THR PRO ASP PHE SER ARG LEU ARG ARG TYR PHE VAL SEQRES 4 A 88 ALA PHE ASP GLY ASP LEU VAL GLN GLU PHE ASP MET THR SEQRES 5 A 88 SER ALA THR HIS VAL LEU GLY SER ARG ASP LYS ASN PRO SEQRES 6 A 88 ALA ALA GLN GLN VAL SER PRO GLU TRP ILE TRP ALA CYS SEQRES 7 A 88 ILE ARG LYS ARG ARG LEU VAL ALA PRO CYS
HELIX 1 1 SER A 836 LEU A 841 1 6 HELIX 2 2 ASP A 864 ASP A 876 1 13 HELIX 3 3 SER A 905 ARG A 916 1 12
SHEET 1 A 2 VAL A 891 LEU A 892 0 SHEET 2 A 2 GLN A 903 VAL A 904 1 N VAL A 904 O VAL A 891
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000