HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 31-DEC-08 2KD1 TITLE SOLUTION NMR STRUCTURE OF THE INTEGRASE-LIKE DOMAIN FROM BACILLUS TITLE 2 CEREUS ORDERED LOCUS BC_1272. NORTHEAST STRUCTURAL GENOMICS TITLE 3 CONSORTIUM TARGET BCR268F COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA INTEGRATION/RECOMBINATION/INVERTION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 61-170; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS ATCC 14579; SOURCE 3 ORGANISM_TAXID: 226900; SOURCE 4 STRAIN: DSM 31; SOURCE 5 ATCC: 14579; SOURCE 6 GENE: BC_1272; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21-23C; SOURCE 12 OTHER_DETAILS: GROWTH MEDIA: MJ9 100%N15 5%C13, MJ9 100%N15 100%C13 KEYWDS PROTEIN STRUCTURE INITIATIVE, STRUCTURAL GENOMICS, UNKNOWN FUNCTION, KEYWDS 2 PSI-2, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.ROSSI,H.LEE,M.MAGLAQUI,E.L.FOOTE,W.A.BUCHWALD,M.JIANG,G.V.T.SWAPNA, AUTHOR 2 R.NAIR,R.XIAO,T.B.ACTON,B.ROST,J.H.PRESTEGARD,G.T.MONTELIONE, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 01-MAY-24 2KD1 1 REMARK REVDAT 2 19-FEB-20 2KD1 1 REMARK SEQADV REVDAT 1 20-JAN-09 2KD1 0 JRNL AUTH P.ROSSI,H.LEE,R.XIAO,T.B.ACTON,J.H.PRESTEGARD,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE INTEGRASE-LIKE DOMAIN FROM JRNL TITL 2 BACILLUS CEREUS ORDERED LOCUS BC_1272. NORTHEAST STRUCTURAL JRNL TITL 3 GENOMICS CONSORTIUM TARGET BCR268F. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, CNS 1.2, PDBSTAT 5.1 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS), TEJERO, MONTELIONE REMARK 3 (PDBSTAT) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MONOMER BY GEL FILTRATION REMARK 3 CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG) (MS) = REMARK 3 592.3/97.44, TAUC = 5.39 (NS). CONSISTENT WITH MOLECULAR WEIGHT. REMARK 3 STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY REMARK 3 ASSIGNMENTS BY CYANA-3.0 WITH RDC. 20 OF 100 STRUCTURES LOWEST REMARK 3 TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE REMARK 3 FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL AND RDC SAMPLE REMARK 3 ALIGNED IN POLYACRYLAMIDE GEL (NILGES PROTOCOL WITH PARAM19). REMARK 3 ASSIGNMENT STATS (ALL RESIDUES INCLUDED): BACKBONE 93.88%, REMARK 3 SIDECHAIN 85.19%, AROMATIC (SC) 92.00%, STEREOSPECIFIC VL METHYL REMARK 3 ASSIGNMENT 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED REMARK 3 ON 2127 NOE, 246 DIHE, 105 RDC. MAX NOE VIOLATION: 0.41 A REMARK 3 (1MODEL); MAX DIHE VIOLATION: 6.1 DEG. TWO TOTAL CLOSE CONTACTS REMARK 3 PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED REMARK 3 RESIDUES RANGES: 7-22, 25-103 FOR [S(PHI)+S(PSI)] > 1.8. REMARK 3 SECONDARY STRUCTURE - ALPHA HELICES: 8-23, 25-35, 39-42, 53-66, REMARK 3 70-89 RMSD (ANG): BACKBONE 0.4, ALL HEAVY ATOMS 0.7. REMARK 3 RAMACHANDRAN DISTRIBUTION: 94.0/6.0/0.0/0.0. PROCHECK (PSI-PHI): REMARK 3 0.28/1.42 (RAW/Z), PROCHECK (ALL): 0.23/1.36 (RAW/Z), MOLPROBITY REMARK 3 CLASH: 14.45/-0.95 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES REMARK 3 (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.97, PRECISION: REMARK 3 0.85, F-MEASURE: 0.91, DP-SCORE: 0.82. RDC STATISTICS FROM CYANA- REMARK 3 3.0. DA = -4.301 HZ, RHOM = 0.3925; CORR. COEFF: 0.947 +/- 0.002, REMARK 3 Q-FACTOR: 32.55 +/- 0.405%. AFTER CNS WATER REFINEMENT WITH RDC REMARK 3 PALES COMPUTED CORRELATION COEFF: 0.913 AND Q-FACTOR: 40.08% REMARK 3 LOWEST ENERGY MODEL. REMARK 4 REMARK 4 2KD1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000100968. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.986 MM [U-100% 13C; U-100% REMARK 210 15N] PROTEIN-1, 50 UM DSS-2, 200 REMARK 210 MM SODIUM CHLORIDE-3, 20 MM MES- REMARK 210 4, 10 MM DTT-5, 0.02 % NAN3-6, 5 REMARK 210 MM CALCIUM CHLORIDE-7, 90% H2O/ REMARK 210 10% D2O; 0.953 MM [5% 13C; U-100% REMARK 210 15N] PROTEIN-8, 50 UM DSS-9, REMARK 210 200 MM SODIUM CHLORIDE-10, 20 MM REMARK 210 MES-11, 10 MM DTT-12, 0.02 % REMARK 210 NAN3-13, 5 MM CALCIUM CHLORIDE- REMARK 210 14, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 13C NOESY; 3D 1H-15N NOESY; 3D REMARK 210 HCCH-COSY; 3D CCH-TOCSY; 3D REMARK 210 HBHA(CO)NH; N15 T1; N15 T2; HET REMARK 210 NOE; N15 TROSY ISO; N15 TROSY REMARK 210 POLYACRYLAMIDE GEL; 2D 1H-13C REMARK 210 HSQC STEREOMETHYLS REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY, PINE, CYANA 3.0 REMARK 210 BETA, TALOS, PSVS, MOLMOL, REMARK 210 PROCHECK, MOLPROBITY REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 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 APPLY THE FOLLOWING TO CHAINS: A 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 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 1 LEU A 35 -70.56 -60.54 REMARK 500 1 ARG A 38 -65.36 -97.32 REMARK 500 1 SER A 42 -72.97 -101.82 REMARK 500 1 LEU A 51 94.70 -62.84 REMARK 500 1 PRO A 104 -178.65 -54.37 REMARK 500 1 LYS A 105 87.50 -55.78 REMARK 500 1 ASP A 107 -155.58 -111.68 REMARK 500 1 HIS A 113 -168.26 -77.50 REMARK 500 1 HIS A 114 49.34 74.80 REMARK 500 2 PRO A 3 96.25 -59.83 REMARK 500 2 SER A 42 -73.44 -108.53 REMARK 500 2 LEU A 51 98.14 -67.47 REMARK 500 2 PRO A 104 -172.48 -63.97 REMARK 500 2 LYS A 105 82.71 -68.67 REMARK 500 2 ALA A 106 54.44 -149.95 REMARK 500 2 HIS A 113 39.48 -86.17 REMARK 500 3 PRO A 3 98.16 -68.16 REMARK 500 3 SER A 4 92.56 -64.25 REMARK 500 3 ARG A 38 -60.31 -97.34 REMARK 500 3 SER A 42 -68.13 -103.89 REMARK 500 3 LEU A 51 92.35 -64.25 REMARK 500 4 PRO A 3 -172.12 -66.03 REMARK 500 4 SER A 4 36.07 -82.65 REMARK 500 4 LEU A 6 106.77 -179.80 REMARK 500 4 SER A 42 -70.49 -83.86 REMARK 500 4 LEU A 51 88.89 -68.22 REMARK 500 4 ASP A 107 -82.35 71.37 REMARK 500 5 ARG A 38 -60.21 -97.87 REMARK 500 5 SER A 42 -71.02 -83.34 REMARK 500 5 LEU A 51 92.44 -67.88 REMARK 500 5 ASP A 107 -165.81 -166.57 REMARK 500 5 HIS A 113 -17.13 71.86 REMARK 500 6 PRO A 3 87.20 -56.40 REMARK 500 6 SER A 42 -73.92 -108.37 REMARK 500 6 LEU A 51 92.97 -62.76 REMARK 500 6 ALA A 106 -168.81 -115.00 REMARK 500 6 GLU A 110 -97.92 58.84 REMARK 500 6 LEU A 111 -53.68 68.88 REMARK 500 6 HIS A 116 43.32 -82.28 REMARK 500 7 SER A 42 -68.16 -104.21 REMARK 500 7 LEU A 51 100.73 -59.93 REMARK 500 7 ASP A 107 110.41 -167.70 REMARK 500 7 LYS A 108 112.49 -169.41 REMARK 500 7 HIS A 115 -70.59 -95.30 REMARK 500 8 LEU A 6 124.27 174.65 REMARK 500 8 SER A 42 -72.81 -100.50 REMARK 500 8 LEU A 51 99.93 -63.22 REMARK 500 8 ASP A 107 -168.58 -121.11 REMARK 500 8 LYS A 108 25.88 -140.82 REMARK 500 8 GLU A 110 32.32 -78.97 REMARK 500 REMARK 500 THIS ENTRY HAS 116 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16102 RELATED DB: BMRB REMARK 900 RELATED ID: BCR268F RELATED DB: TARGETDB DBREF 2KD1 A 2 111 UNP Q81GD4 Q81GD4_BACCR 61 170 SEQADV 2KD1 MET A 1 UNP Q81GD4 EXPRESSION TAG SEQADV 2KD1 GLU A 112 UNP Q81GD4 EXPRESSION TAG SEQADV 2KD1 HIS A 113 UNP Q81GD4 EXPRESSION TAG SEQADV 2KD1 HIS A 114 UNP Q81GD4 EXPRESSION TAG SEQADV 2KD1 HIS A 115 UNP Q81GD4 EXPRESSION TAG SEQADV 2KD1 HIS A 116 UNP Q81GD4 EXPRESSION TAG SEQADV 2KD1 HIS A 117 UNP Q81GD4 EXPRESSION TAG SEQADV 2KD1 HIS A 118 UNP Q81GD4 EXPRESSION TAG SEQRES 1 A 118 MET GLU PRO SER LYS LEU SER TYR GLY GLU TYR LEU GLU SEQRES 2 A 118 SER TRP PHE ASN THR LYS ARG HIS SER VAL GLY ILE GLN SEQRES 3 A 118 THR ALA LYS VAL LEU LYS GLY TYR LEU ASN SER ARG ILE SEQRES 4 A 118 ILE PRO SER LEU GLY ASN ILE LYS LEU ALA LYS LEU THR SEQRES 5 A 118 SER LEU HIS MET GLN ASN TYR VAL ASN SER LEU ARG ASP SEQRES 6 A 118 GLU GLY LEU LYS ARG GLY THR ILE GLU LYS ILE ILE LYS SEQRES 7 A 118 VAL ILE ARG ASN SER LEU GLU HIS ALA ILE ASP LEU GLU SEQRES 8 A 118 LEU ILE THR LYS ASN VAL ALA ALA LYS THR LYS LEU PRO SEQRES 9 A 118 LYS ALA ASP LYS GLU GLU LEU GLU HIS HIS HIS HIS HIS SEQRES 10 A 118 HIS HELIX 1 1 SER A 7 GLY A 24 1 18 HELIX 2 2 GLY A 24 ASN A 36 1 13 HELIX 3 3 ARG A 38 LEU A 43 1 6 HELIX 4 4 LYS A 47 LEU A 51 5 5 HELIX 5 5 THR A 52 GLY A 67 1 16 HELIX 6 6 LYS A 69 LEU A 90 1 22 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 MODEL 1