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- PDB-5x4h: The crystal structure of Pyrococcus furiosus RecJ (wild-type) -

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Basic information

Entry
Database: PDB / ID: 5x4h
TitleThe crystal structure of Pyrococcus furiosus RecJ (wild-type)
ComponentsUncharacterized protein
KeywordsHYDROLASE / Archaeal RecJ / CMG interaction domain / Nuclease activity / GINS / interaction
Function / homology
Function and homology information


exonuclease activity / nucleic acid binding / metal ion binding
Similarity search - Function
: / DHH-CID domain / : / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.801 Å
AuthorsLi, M.J. / Yi, G.S. / Yu, F. / Zhou, H. / Chen, J.N. / Xu, C.Y. / Wang, F.P. / Xiao, X. / He, J.H. / Liu, X.P.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The crystal structure of Pyrococcus furiosus RecJ implicates it as an ancestor of eukaryotic Cdc45.
Authors: Li, M.J. / Yi, G.S. / Yu, F. / Zhou, H. / Chen, J.N. / Xu, C.Y. / Wang, F.P. / Xiao, X. / He, J.H. / Liu, X.P.
History
DepositionFeb 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4482
Polymers56,4241
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area18980 Å2
Unit cell
Length a, b, c (Å)58.409, 66.625, 59.857
Angle α, β, γ (deg.)90.00, 112.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein / RecJ


Mass: 56423.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF2055 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZE0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.74 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 4.3% w/v PEG 2000 MME, 50 mM Bicine pH 8.8, 28.6% w/v PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 10538 / % possible obs: 99.9 % / Redundancy: 7.5 % / Net I/σ(I): 26.4
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 10.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.801→49.033 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.76
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2233 576 5.47 %
Rwork0.2065 --
obs0.2075 10538 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.801→49.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3705 0 1 0 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023779
X-RAY DIFFRACTIONf_angle_d0.425095
X-RAY DIFFRACTIONf_dihedral_angle_d12.9142292
X-RAY DIFFRACTIONf_chiral_restr0.039564
X-RAY DIFFRACTIONf_plane_restr0.002664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8012-3.08310.28271480.24962420X-RAY DIFFRACTION98
3.0831-3.52910.25231750.22932477X-RAY DIFFRACTION100
3.5291-4.44580.20881280.18752513X-RAY DIFFRACTION100
4.4458-49.04030.17681250.18842552X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2672-0.28631.00392.00781.27944.0628-0.077-0.8101-0.01830.75180.09110.20660.1993-0.6852-0.00020.2837-0.0401-0.08480.3161-0.02670.166182.4562-0.0979140.9593
22.6893-0.76021.24232.0448-0.50483.1409-0.2815-0.74250.27240.76990.12960.2409-0.2939-0.78060.09590.38620.006-0.01140.4607-0.10110.278678.39937.7126140.1574
32.6385-1.31741.35331.4653-0.80422.71160.00370.14370.1868-0.0766-0.13750.1063-0.02670.17350.07980.1009-0.01070.01070.08380.01440.071375.04395.515109.5521
43.5178-0.1397-0.41561.50050.09181.7303-0.004-0.1559-0.08490.2450.06980.27640.0186-0.311-0.00880.17150.03290.02630.17550.05460.13164.5832-4.5482125.4592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 95 )
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 148 )
3X-RAY DIFFRACTION3chain 'A' and (resid 149 through 281 )
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 469 )

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