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- PDB-3nrw: Crystal Structure of the N-terminal domain of Phage integrase/sit... -

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Basic information

Entry
Database: PDB / ID: 3nrw
TitleCrystal Structure of the N-terminal domain of Phage integrase/site-specific recombinase (tnp) from Haloarcula marismortui, Northeast Structural Genomics Consortium Target HmR208A
ComponentsPhage integrase/site-specific recombinase
KeywordsRECOMBINATION / alpha-helical domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


DNA integration / DNA recombination / DNA binding
Similarity search - Function
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
Phage integrase/site-specific recombinase
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsForouhar, F. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HmR208A
Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage integrase/site-specific recombinase


Theoretical massNumber of molelcules
Total (without water)14,0521
Polymers14,0521
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.531, 78.531, 36.654
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Phage integrase/site-specific recombinase


Mass: 14052.396 Da / Num. of mol.: 1 / Fragment: N-terminal domain residues 1-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / Gene: rrnAC0581, tnp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q5V4F9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 277 K / pH: 5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 0.1M Sodium Acetate (pH 5), 2.99M NaCl, and 20% glycerol as cryo-protectant, Microbatch, under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97901 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 27811 / Num. obs: 23807 / % possible obs: 85.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.044 / Net I/σ(I): 43.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 6.3 / Rsym value: 0.185 / % possible all: 57.9

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Processing

Software
NameVersionClassificationNB
CNS1.2 & XtalViewrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXfollowed by model building by Arpphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.203 2207 7.9 %
Rwork0.186 --
all0.189 27788 -
obs0.187 23787 85.6 %
Solvent computationBsol: 49.589 Å2
Displacement parametersBiso max: 62.83 Å2 / Biso mean: 25.275 Å2 / Biso min: 9.65 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å20 Å2
2---2.4 Å20 Å2
3---4.801 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms867 0 0 106 973
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it3.0051.5
X-RAY DIFFRACTIONc_scbond_it5.2552
X-RAY DIFFRACTIONc_mcangle_it3.7572
X-RAY DIFFRACTIONc_scangle_it6.8912.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.236 138 -
Rwork0.221 --
obs-1453 57.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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