[English] 日本語
Yorodumi
- PDB-3crw: XPD_APO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3crw
TitleXPD_APO
ComponentsXPD/Rad3 related DNA helicase
KeywordsHYDROLASE / XPD Helicase DNA Repair Cancer Aging / Helicase
Function / homology
Function and homology information


DNA duplex unwinding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / DNA helicase / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Fumarase C; Chain B, domain 1 - #30 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 ...Fumarase C; Chain B, domain 1 - #30 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / Fumarase C; Chain B, domain 1 / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HEXACYANOFERRATE(3-) / ATP-dependent DNA helicase Saci_0192
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsFan, L. / Arvai, A.S. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations.
Authors: Fan, L. / Fuss, J.O. / Cheng, Q.J. / Arvai, A.S. / Hammel, M. / Roberts, V.A. / Cooper, P.K. / Tainer, J.A.
History
DepositionApr 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity_src_gen / struct
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _struct.title
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: XPD/Rad3 related DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2982
Polymers64,0861
Non-polymers2121
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.383, 69.805, 145.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein XPD/Rad3 related DNA helicase


Mass: 64086.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: Saci_0192 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q4JC68, Hydrolases
#2: Chemical ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6FeN6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 0.4M Citrate pH 5.6 15-20% PEG 4000 10% Isopropanol, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11583 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: ALS 12.3.1
RadiationMonochromator: ALS 12.3.1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.98→43 Å / Num. obs: 9404 / % possible obs: 81.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 0 Å2
Reflection shellResolution: 2.98→3.11 Å / % possible all: 37.7

-
Processing

Software
NameVersionClassificationNB
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CRV

3crv


Resolution: 4→43 Å / Rfactor Rfree error: 0.017 / Occupancy max: 1 / Occupancy min: 1 / Stereochemistry target values: Engh & Huber
Details: CROSS-VALIDATION METHOD: -> " THROUGHOUT" FREE R VALUE TEST SET SELECTION CRITERIA: -> " RANDOM" NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. POLYMER 3973 NONPOLYMER 13 SOLVENT 73 CNS ...Details: CROSS-VALIDATION METHOD: -> " THROUGHOUT" FREE R VALUE TEST SET SELECTION CRITERIA: -> " RANDOM" NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. POLYMER 3973 NONPOLYMER 13 SOLVENT 73 CNS PARAMETER FILES: CNS_TOPPAR/PROTEIN_REP.PARAM CNS_TOPPAR/WATER.PARAM CNS_ TOPPAR/ION.PARAM FEC6.PAR CNS TOPOLOGY FILES: CNS_TOPPAR/ PROTEIN.TOP CNS_TOPPAR/CARBOHYDRATE.TOP CNS_TOPPAR/ION.TOP FEC6.PAR
RfactorNum. reflection% reflection
Rfree0.319 367 7.6 %
Rwork0.237 --
obs0.237 9013 98.4 %
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 103.52 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 111.66 Å2
Baniso -1Baniso -2Baniso -3
1--16.6 Å20 Å20 Å2
2---45.47 Å20 Å2
3---62.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 4→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 13 73 4059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg4.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 4→4.18 Å / Rfactor Rfree error: 0.051
RfactorNum. reflection% reflection
Rfree0.323 40 6.8 %
Rwork0.2 548 -
obs--97.7 %

+
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://pdbjlvh1.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