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- PDB-2kd1: Solution NMR structure of the integrase-like domain from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 2kd1
TitleSolution NMR structure of the integrase-like domain from Bacillus cereus ordered locus BC_1272. Northeast Structural Genomics Consortium Target BcR268F
ComponentsDNA integration/recombination/invertion protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / PSI-2 / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


DNA integration / DNA recombination / DNA binding
Similarity search - Function
AP2-like integrase, N-terminal domain / Arm DNA-binding domain / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / Tyrosine recombinase, N-terminal domain / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core ...AP2-like integrase, N-terminal domain / Arm DNA-binding domain / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / Tyrosine recombinase, N-terminal domain / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA integration/recombination/invertion protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsRossi, P. / Lee, H. / Maglaqui, M. / Foote, E.L. / Buchwald, W.A. / Jiang, M. / Swapna, G.V.T. / Nair, R. / Xiao, R. / Acton, T.B. ...Rossi, P. / Lee, H. / Maglaqui, M. / Foote, E.L. / Buchwald, W.A. / Jiang, M. / Swapna, G.V.T. / Nair, R. / Xiao, R. / Acton, T.B. / Rost, B. / Prestegard, J.H. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the Integrase-Like Domain from Bacillus cereus Ordered Locus BC_1272. Northeast Structural Genomics Consortium Target BcR268F.
Authors: Rossi, P. / Lee, H. / Xiao, R. / Acton, T.B. / Prestegard, J.H. / Montelione, G.T.
History
DepositionDec 31, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA integration/recombination/invertion protein


Theoretical massNumber of molelcules
Total (without water)13,5711
Polymers13,5711
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA integration/recombination/invertion protein


Mass: 13570.714 Da / Num. of mol.: 1 / Fragment: UNP residues 61-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: DSM 31
Description: Growth media: MJ9 100%N15 5%C13, MJ9 100%N15 100%C13
Gene: BC_1272 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q81GD4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-13C NOESY
1913D 1H-15N NOESY
11013D (H)CCH-COSY
11113D CCH-TOCSY
11213D HBHA(CO)NH
11322D 1H-15N HSQC
1142N15 T1
1152N15 T2
1162HET noe
1172N15 TROSY iso
1182N15 TROSY PolyAcrylamide Gel
11922D 1H-13C HSQC stereomethyls

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Sample preparation

Details
Solution-IDContentsSolvent system
10.986 mM [U-100% 13C; U-100% 15N] protein-1, 50 uM DSS-2, 200 mM sodium chloride-3, 20 mM MES-4, 10 mM DTT-5, 0.02 % NaN3-6, 5 mM Calcium Chloride-7, 90% H2O/10% D2O90% H2O/10% D2O
20.953 mM [5% 13C; U-100% 15N] protein-8, 50 uM DSS-9, 200 mM sodium chloride-10, 20 mM MES-11, 10 mM DTT-12, 0.02 % NaN3-13, 5 mM Calcium Chloride-14, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.986 mMprotein-1[U-100% 13C; U-100% 15N]1
50 uMDSS-21
200 mMsodium chloride-31
20 mMMES-41
10 mMDTT-51
0.02 %NaN3-61
5 mMCalcium Chloride-71
0.953 mMentity-8[5% 13C; U-100% 15N]2
50 uMDSS-92
200 mMsodium chloride-102
20 mMMES-112
10 mMDTT-122
0.02 %NaN3-132
5 mMCalcium Chloride-142
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
CYANA3.0 betaGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxgeometry optimization
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVSBhattacharya and Montelionevalidation
MOLMOLKoradi, Billeter and Wuthrichvisualization
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thovalidation
PdbStat5.1Tejero, Montelionerefinement
MolProbityRichardsonprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG) (MS) = 592.3/97.44, TAUC = 5.39 (NS). CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE DETERMINED BY TRIPLE ...Details: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG) (MS) = 592.3/97.44, TAUC = 5.39 (NS). CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA-3.0 WITH RDC. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL AND RDC SAMPLE ALIGNED IN POLYACRYLAMIDE GEL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (ALL RESIDUES INCLUDED): BACKBONE 93.88%, SIDECHAIN 85.19%, AROMATIC (SC) 92.00%, STEREOSPECIFIC VL METHYL ASSIGNMENT 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 2127 NOE, 246 DIHE, 105 RDC. MAX NOE VIOLATION: 0.41 A (1MODEL); MAX DIHE VIOLATION: 6.1 DEG. TWO TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 7-22, 25-103 FOR [S(PHI)+S(PSI)] > 1.8. SECONDARY STRUCTURE - ALPHA HELICES: 8-23, 25-35, 39-42, 53-66, 70-89 RMSD (ANG): BACKBONE 0.4, ALL HEAVY ATOMS 0.7. RAMACHANDRAN DISTRIBUTION: 94.0/6.0/0.0/0.0. PROCHECK (PSI-PHI): 0.28/1.42 (RAW/Z), PROCHECK (ALL): 0.23/1.36 (RAW/Z), MOLPROBITY CLASH: 14.45/-0.95 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.97, PRECISION: 0.85, F-MEASURE: 0.91, DP-SCORE: 0.82. RDC STATISTICS FROM CYANA-3.0. DA = -4.301 HZ, RHOM = 0.3925; CORR. COEFF: 0.947 +/- 0.002, Q-FACTOR: 32.55 +/- 0.405%. AFTER CNS WATER REFINEMENT WITH RDC PALES COMPUTED CORRELATION COEFF: 0.913 AND Q-FACTOR: 40.08% LOWEST ENERGY MODEL.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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