[English] 日本語
Yorodumi
- PDB-5x4k: The complex crystal structure of Pyrococcus furiosus RecJ and CMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x4k
TitleThe complex crystal structure of Pyrococcus furiosus RecJ and CMP
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
CYTIDINE-5'-MONOPHOSPHATE / Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 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 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5467
Polymers56,3801
Non-polymers1,1666
Water8,197455
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-112 kcal/mol
Surface area18360 Å2
Unit cell
Length a, b, c (Å)58.426, 66.172, 59.929
Angle α, β, γ (deg.)90.00, 112.22, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Uncharacterized protein / RecJ


Mass: 56379.930 Da / Num. of mol.: 1 / Mutation: D83A
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.39 %
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

-
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: 1.749→50 Å / Num. obs: 72646 / % possible obs: 97.9 % / Redundancy: 7.5 % / Net I/σ(I): 27.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 4.6 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X4J

5x4j


Resolution: 1.749→49.107 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.47 / Phase error: 18.75
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.1888 3584 4.93 %
Rwork0.163 --
obs0.1643 72646 86.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.749→49.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 66 455 4229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033856
X-RAY DIFFRACTIONf_angle_d0.6245208
X-RAY DIFFRACTIONf_dihedral_angle_d14.8762327
X-RAY DIFFRACTIONf_chiral_restr0.043578
X-RAY DIFFRACTIONf_plane_restr0.003668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7488-1.77180.2816690.28051371X-RAY DIFFRACTION44
1.7718-1.7960.2928790.24371562X-RAY DIFFRACTION52
1.796-1.82170.2499860.21651746X-RAY DIFFRACTION56
1.8217-1.84890.2473980.19511881X-RAY DIFFRACTION61
1.8489-1.87780.246820.17962089X-RAY DIFFRACTION67
1.8778-1.90860.2071090.17462231X-RAY DIFFRACTION73
1.9086-1.94150.1811330.16992411X-RAY DIFFRACTION78
1.9415-1.97680.19141020.17142507X-RAY DIFFRACTION83
1.9768-2.01480.20821230.17362663X-RAY DIFFRACTION86
2.0148-2.05590.181460.18272737X-RAY DIFFRACTION89
2.0559-2.10060.17071300.17482801X-RAY DIFFRACTION92
2.1006-2.14950.19381200.16142929X-RAY DIFFRACTION93
2.1495-2.20330.21451650.16572946X-RAY DIFFRACTION95
2.2033-2.26280.17131950.16962864X-RAY DIFFRACTION97
2.2628-2.32940.20781590.1623015X-RAY DIFFRACTION97
2.3294-2.40460.18871880.1682986X-RAY DIFFRACTION98
2.4046-2.49050.2081780.17572967X-RAY DIFFRACTION98
2.4905-2.59020.20481630.17153042X-RAY DIFFRACTION99
2.5902-2.70810.21341890.1612984X-RAY DIFFRACTION99
2.7081-2.85090.20341480.17013076X-RAY DIFFRACTION99
2.8509-3.02950.20681620.16723024X-RAY DIFFRACTION99
3.0295-3.26330.17321730.16813028X-RAY DIFFRACTION99
3.2633-3.59170.17521890.15073003X-RAY DIFFRACTION99
3.5917-4.11120.14851170.13713095X-RAY DIFFRACTION99
4.1112-5.17870.15531460.12813059X-RAY DIFFRACTION99
5.1787-49.12620.18831350.17353045X-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)
12.252-0.48350.76561.41410.00711.51150.0115-0.4877-0.03710.18340.0439-0.00030.0744-0.2322-0.03250.1214-0.0268-0.00230.1791-0.01120.109380.6139-4.6051141.3022
21.06790.05511.11070.43880.1452.1585-0.01860.06370.1212-0.07850.0144-0.0037-0.02670.01790.01480.1115-0.00720.01790.07550.01240.110376.1385-0.8801111.6638
32.3580.129-0.39160.67520.27730.6639-0.04580.0497-0.080.0814-0.00440.0570.0888-0.06740.05230.12740.00310.00390.0757-0.00920.080164.3641-11.3245125.2771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 135 )
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 281 )
3X-RAY DIFFRACTION3chain 'A' and (resid 282 through 469 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more