[English] 日本語
Yorodumi
- PDB-4fzo: Crystal Structure of the apo-form uranyl binding protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fzo
TitleCrystal Structure of the apo-form uranyl binding protein
Componentsuranyl binding protein
KeywordsUNKNOWN FUNCTION / uranyl binding / uranyl
Function / homologyDomain of unknown function DUF357 / AF1782-like superfamily / Protein of unknown function (DUF357) / AF1782-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha / DUF357 domain-containing protein
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHe, C. / Zhou, L. / Zhang, L.
CitationJournal: Nat Chem / Year: 2014
Title: A protein engineered to bind uranyl selectively and with femtomolar affinity.
Authors: Zhou, L. / Bosscher, M. / Zhang, C. / Ozcubukcu, S. / Zhang, L. / Zhang, W. / Li, C.J. / Liu, J. / Jensen, M.P. / Lai, L. / He, C.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uranyl binding protein
B: uranyl binding protein


Theoretical massNumber of molelcules
Total (without water)19,0852
Polymers19,0852
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-19 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.256, 47.034, 65.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein uranyl binding protein


Mass: 9542.686 Da / Num. of mol.: 2 / Mutation: L13D, D17E, H64E, L67T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: MTH_1690 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / References: UniProt: O27725
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.78 Å3/Da / Density % sol: 31.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 3350, Tacsimate 4.0, sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.3→38.2 Å / Num. all: 34522 / Num. obs: 34522 / % possible obs: 15.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 7.69 Å2
Reflection shellResolution: 1.3→1.35 Å / % possible all: 89.2

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→38.193 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.11 / σ(F): 1.39 / Phase error: 15.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1756 1715 5.07 %
Rwork0.1596 --
obs0.1604 33856 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.305 Å2
Baniso -1Baniso -2Baniso -3
1-0.3178 Å2-0 Å2-0 Å2
2---0.3014 Å2-0 Å2
3----0.0165 Å2
Refinement stepCycle: LAST / Resolution: 1.3→38.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 0 183 1497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071387
X-RAY DIFFRACTIONf_angle_d1.0941875
X-RAY DIFFRACTIONf_dihedral_angle_d13.524562
X-RAY DIFFRACTIONf_chiral_restr0.076212
X-RAY DIFFRACTIONf_plane_restr0.004245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.33560.19111280.15582307X-RAY DIFFRACTION86
1.3356-1.37870.18531310.1592629X-RAY DIFFRACTION97
1.3787-1.4280.20741370.15952677X-RAY DIFFRACTION99
1.428-1.48510.16111550.15672673X-RAY DIFFRACTION100
1.4851-1.55270.14121370.14182699X-RAY DIFFRACTION100
1.5527-1.63460.16041380.14262698X-RAY DIFFRACTION100
1.6346-1.7370.1641490.15082700X-RAY DIFFRACTION100
1.737-1.87110.16811300.16012714X-RAY DIFFRACTION99
1.8711-2.05940.19711650.15912686X-RAY DIFFRACTION100
2.0594-2.35740.18211330.15352750X-RAY DIFFRACTION99
2.3574-2.96990.16671620.16582747X-RAY DIFFRACTION99
2.9699-38.20970.1811500.1712861X-RAY DIFFRACTION98

+
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