[English] 日本語
Yorodumi
- PDB-2o9x: Crystal Structure Of A Putative Redox Enzyme Maturation Protein F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o9x
TitleCrystal Structure Of A Putative Redox Enzyme Maturation Protein From Archaeoglobus Fulgidus
ComponentsReductase, assembly protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SAD / RAMP / HELICAL PROTEIN / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


putative redox-enzyme maturation protein fold / putative redox-enzyme maturation protein domain / nitrate reductase, subunit delta (NarJ) / : / : / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle ...putative redox-enzyme maturation protein fold / putative redox-enzyme maturation protein domain / nitrate reductase, subunit delta (NarJ) / : / : / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Reductase, assembly protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsKirillova, O. / Chruszcz, M. / Skarina, T. / Gorodichtchenskaia, E. / Cymborowski, M. / Shumilin, I. / Savchenko, A. / Edwards, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: An extremely SAD case: structure of a putative redox-enzyme maturation protein from Archaeoglobus fulgidus at 3.4 A resolution.
Authors: Kirillova, O. / Chruszcz, M. / Shumilin, I.A. / Skarina, T. / Gorodichtchenskaia, E. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
SupersessionMar 13, 2007ID: 1ZE0
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reductase, assembly protein


Theoretical massNumber of molelcules
Total (without water)20,9571
Polymers20,9571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Reductase, assembly protein

A: Reductase, assembly protein


Theoretical massNumber of molelcules
Total (without water)41,9142
Polymers41,9142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area2160 Å2
ΔGint-18 kcal/mol
Surface area14550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)137.510, 137.510, 64.282
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Reductase, assembly protein


Mass: 20957.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0173 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: O30064

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.6 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 3.9
Details: 2.5 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K, pH 3.90

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2004 / Details: SI 111 CHANNEL
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.97931
ReflectionResolution: 3.4→50 Å / Num. all: 5295 / Num. obs: 5292 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 24.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 36.95
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 26.1 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 5.18 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
SOLVERESOLVEphasing
Omodel building
Cootmodel building
CCP4model building
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-3000phasing
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 3.4→34.38 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / SU B: 42.823 / SU ML: 0.324 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.245 / ESU R Free: 0.468
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 254 4.8 %RANDOM
Rwork0.237 ---
all0.239 5008 --
obs0.239 5008 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 77.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å2-1 Å20 Å2
2---2.01 Å20 Å2
3---3.01 Å2
Refinement stepCycle: LAST / Resolution: 3.4→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 0 0 1130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211162
X-RAY DIFFRACTIONr_angle_refined_deg2.511.9441595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4115161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23222.95544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.84815118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.1153
X-RAY DIFFRACTIONr_chiral_restr0.1540.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02938
X-RAY DIFFRACTIONr_nbd_refined0.3080.2725
X-RAY DIFFRACTIONr_nbtor_refined0.3540.2808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.22
X-RAY DIFFRACTIONr_mcbond_it3.2653824
X-RAY DIFFRACTIONr_mcangle_it6.02151249
X-RAY DIFFRACTIONr_scbond_it9.2568398
X-RAY DIFFRACTIONr_scangle_it13.27411346
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.536 13 -
Rwork0.326 363 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 37.561 Å / Origin y: 39.856 Å / Origin z: 35.883 Å
111213212223313233
T0.0146 Å20.1507 Å20.0925 Å2--0.0038 Å20.139 Å2---0.066 Å2
L1.8271 °21.0578 °21.4473 °2-2.0688 °21.4985 °2--3.4787 °2
S0.2461 Å °-0.2479 Å °0.0106 Å °0.1732 Å °-0.1181 Å °0.1796 Å °0.5354 Å °-0.0808 Å °-0.128 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-5 - 5517 - 77
2X-RAY DIFFRACTION1AA65 - 15187 - 173

+
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