[English] 日本語
Yorodumi
- PDB-4y2i: Gold ion bound to GolB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y2i
TitleGold ion bound to GolB
ComponentsPutative metal-binding transport protein
KeywordsMETAL TRANSPORT / Gold binding protein
Function / homology
Function and homology information


Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Putative metal-binding transport protein / :
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsWei, W. / Wang, F. / Ma, L. / Zhao, J.
Funding support China, 3items
OrganizationGrant numberCountry
the National Science Foundation of China21332005 China
the MOST of China2014AA020512 China
the National Natural Science Foundation of China31200607 China
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Structural Insights and the Surprisingly Low Mechanical Stability of the Au-S Bond in the Gold-Specific Protein GolB
Authors: Wei, W. / Sun, Y. / Zhu, M. / Liu, X. / Sun, P. / Wang, F. / Gui, Q. / Meng, W. / Cao, Y. / Zhao, J.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative metal-binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3223
Polymers6,9281
Non-polymers3942
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-9 kcal/mol
Surface area3850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.093, 37.093, 169.911
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Putative metal-binding transport protein / GolB


Mass: 6927.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: DT2 / Gene: STMDT2_03511 / Production host: Escherichia coli (E. coli) / References: UniProt: U4MDP1, UniProt: A0A140UHB4*PLUS
#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M Ammonium citrate tribasic, 0.1 M BIS-TRIS propane

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 7169 / % possible obs: 99 % / Redundancy: 10.6 % / Net I/σ(I): 51
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.2 / % possible all: 86.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→31.56 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.889 / SU B: 3.623 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26638 240 4.6 %RANDOM
Rwork0.22678 ---
obs0.22867 5003 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms481 0 2 34 517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019494
X-RAY DIFFRACTIONr_bond_other_d0.0010.02501
X-RAY DIFFRACTIONr_angle_refined_deg0.8531.972670
X-RAY DIFFRACTIONr_angle_other_deg0.51531140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.596566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14124.21119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5341588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.542154
X-RAY DIFFRACTIONr_chiral_restr0.0470.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021554
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02100
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5762.07261
X-RAY DIFFRACTIONr_mcbond_other2.5792.063260
X-RAY DIFFRACTIONr_mcangle_it4.0973.073325
X-RAY DIFFRACTIONr_mcangle_other4.0943.079326
X-RAY DIFFRACTIONr_scbond_it3.8312.53233
X-RAY DIFFRACTIONr_scbond_other3.8232.538234
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9283.571344
X-RAY DIFFRACTIONr_long_range_B_refined8.75116.612539
X-RAY DIFFRACTIONr_long_range_B_other8.74816.454533
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 15 -
Rwork0.284 360 -
obs--98.43 %

+
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