[English] 日本語
Yorodumi
- PDB-3ov8: Crystal structure of AF1382 from Archaeoglobus fulgidus, High res... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ov8
TitleCrystal structure of AF1382 from Archaeoglobus fulgidus, High resolution
ComponentsProtein AF_1382
KeywordsUNKNOWN FUNCTION / AF1382 / PSI / STRUCTURAL GENOMICS / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / putative DNS binding
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / ACETATE ION / Uncharacterized protein AF_1382
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8501 Å
AuthorsZhu, J.-Y. / Zhao, M. / Fu, Z.-Q. / Yang, H. / Chang, J. / Hao, X. / Chen, L. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal.
Authors: Zhu, J.Y. / Fu, Z.Q. / Chen, L. / Xu, H. / Chrzas, J. / Rose, J. / Wang, B.C.
History
DepositionSep 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Atomic model / Data collection
Revision 1.2Jul 4, 2012Group: Database references
Revision 1.3Sep 19, 2012Group: Database references
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein AF_1382
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2894
Polymers11,1591
Non-polymers1303
Water1,36976
1
A: Protein AF_1382
hetero molecules

A: Protein AF_1382
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5788
Polymers22,3182
Non-polymers2606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3290 Å2
ΔGint-48 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.033, 53.033, 40.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11A-105-

HOH

-
Components

#1: Protein Protein AF_1382


Mass: 11159.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF1382, AF_1382 / Plasmid: pDEST-527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RPX / References: UniProt: O28889
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.7 Å3/Da / Density % sol: 54.4 % / Description: STARTING MODEL FROM SULFUR SAD
Crystal growTemperature: 291 K / Method: modified macrobatch / pH: 4.6
Details: Microbatch using 1.0 microliter drops containing equal volumes of protein concentrate (2.8 mg/ml) and solution containg 0.2 M ammonium sulfate, 0.1 M sodium acetate, 30% w/v polyethylene ...Details: Microbatch using 1.0 microliter drops containing equal volumes of protein concentrate (2.8 mg/ml) and solution containg 0.2 M ammonium sulfate, 0.1 M sodium acetate, 30% w/v polyethylene glycol monomethyl ether, temperature 291k, pH 4.6, modified macrobatch

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 / Wavelength: 0.974 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97241
20.9741
ReflectionResolution: 1.85→50 Å / Num. all: 9876 / Num. obs: 9859 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rsym value: 0.051 / Net I/σ(I): 60.66
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 12.96 / Rsym value: 0.233 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.3phasing
SERGUIdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3O3K

3o3k


Resolution: 1.8501→37.5 Å / SU ML: 0.21 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Phase error: 20.06 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.2145 493 5.05 %
Rwork0.1786 --
obs0.1804 9761 98.97 %
all-9876 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.004 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5977 Å2-0 Å20 Å2
2---0.5977 Å2-0 Å2
3---1.1953 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8501→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 6 76 830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008774
X-RAY DIFFRACTIONf_angle_d0.9981038
X-RAY DIFFRACTIONf_dihedral_angle_d14.608307
X-RAY DIFFRACTIONf_chiral_restr0.067118
X-RAY DIFFRACTIONf_plane_restr0.003128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-2.03630.25011170.20712270X-RAY DIFFRACTION97
2.0363-2.33090.24171270.17542290X-RAY DIFFRACTION99
2.3309-2.93650.23951230.1762339X-RAY DIFFRACTION100
2.9365-37.50770.18811260.17552369X-RAY DIFFRACTION100
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)
11.6152-1.4809-1.25431.6931.50281.4278-0.5176-0.0556-0.6056-0.2629-0.0680.80.2059-0.06160.55040.48530.03-0.00570.1146-0.04110.2874-6.146526.075512.7178
20.45110.10390.01940.0483-0.08591.02780.03890.0309-0.13370.0285-0.02710.03480.0416-0.2159-0.01220.1566-0.01320.0150.044-0.01790.117-0.83759.321617.3476
31.60790.7326-0.3723.66591.23961.5714-0.01170.209-0.0951-0.304-0.0987-0.4644-0.45140.07590.10080.2076-0.02060.00580.15050.01840.1688.071813.46089.9226
41.231-0.3873-0.32242.598-0.5020.8437-0.2124-0.0086-0.08840.69340.14440.07430.14790.06140.08780.2264-0.0413-0.01740.0563-0.0130.10622.929415.084121.3403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:12)
2X-RAY DIFFRACTION2(chain A and resid 13:41)
3X-RAY DIFFRACTION3(chain A and resid 42:58)
4X-RAY DIFFRACTION4(chain A and resid 59:94)
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6act.paract.top

+
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