[English] 日本語
Yorodumi
- PDB-6cmk: Crystal structure of Citrobacter koseri AztD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cmk
TitleCrystal structure of Citrobacter koseri AztD
ComponentsAztD protein
KeywordsMETAL BINDING PROTEIN / zinc / beta propeller / periplasm
Function / homology: / Nitrous oxide reductase, N-terminal / periplasmic space / WD40/YVTN repeat-like-containing domain superfamily / metal ion binding / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Zinc chaperone AztD
Function and homology information
Biological speciesCitrobacter koseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.732 Å
AuthorsYukl, E.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)SC2GM111170 United States
CitationJournal: Commun Biol / Year: 2019
Title: Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins.
Authors: Neupane, D.P. / Fullam, S.H. / Chacon, K.N. / Yukl, E.T.
History
DepositionMar 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: AztD protein
A: AztD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,09114
Polymers90,9352
Non-polymers1,15712
Water12,070670
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-125 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.230, 128.790, 56.850
Angle α, β, γ (deg.)90.00, 105.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein AztD protein


Mass: 45467.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) (bacteria)
Strain: ATCC BAA-895 / CDC 4225-83 / SGSC4696 / Gene: CKO_00948 / Plasmid: pCDF Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8AF35

-
Non-polymers , 6 types, 682 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 292 K / Method: batch mode / pH: 6
Details: 10 mg/mL protein was combined in a 1:1 ratio with 24% PEG 4000, 0.1 M sodium nitrate, 0.1 M MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→64.4 Å / Num. obs: 77405 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.04 / Rrim(I) all: 0.073 / Net I/σ(I): 10.2
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4202 / CC1/2: 0.868 / Rpim(I) all: 0.237 / Rrim(I) all: 0.438 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.732→64.395 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.78
RfactorNum. reflection% reflection
Rfree0.1884 1997 2.58 %
Rwork0.153 --
obs0.154 77292 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.8 Å2
Refinement stepCycle: LAST / Resolution: 1.732→64.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5658 0 61 670 6389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055935
X-RAY DIFFRACTIONf_angle_d0.9478073
X-RAY DIFFRACTIONf_dihedral_angle_d12.2643561
X-RAY DIFFRACTIONf_chiral_restr0.061914
X-RAY DIFFRACTIONf_plane_restr0.0061056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.732-1.77530.2581570.20325324X-RAY DIFFRACTION99
1.7753-1.82330.26391330.19045323X-RAY DIFFRACTION99
1.8233-1.8770.21941400.17765387X-RAY DIFFRACTION99
1.877-1.93760.27281450.175356X-RAY DIFFRACTION99
1.9376-2.00680.18851450.15945287X-RAY DIFFRACTION98
2.0068-2.08720.18791360.15715386X-RAY DIFFRACTION100
2.0872-2.18220.1951430.15245408X-RAY DIFFRACTION100
2.1822-2.29720.17491370.14815344X-RAY DIFFRACTION99
2.2972-2.44120.18991450.1525331X-RAY DIFFRACTION98
2.4412-2.62960.21721480.15665425X-RAY DIFFRACTION100
2.6296-2.89430.19211390.15645401X-RAY DIFFRACTION100
2.8943-3.31310.19951460.15545404X-RAY DIFFRACTION99
3.3131-4.1740.16151480.13855443X-RAY DIFFRACTION100
4.174-64.43950.15611350.14215476X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.8527 Å / Origin y: -1.5174 Å / Origin z: -2.614 Å
111213212223313233
T0.092 Å2-0.0056 Å20.0092 Å2-0.1251 Å2-0.0104 Å2--0.1085 Å2
L0.5136 °2-0.0457 °20.0332 °2-0.783 °2-0.0021 °2--0.6056 °2
S0.0045 Å °0.0178 Å °-0.0107 Å °-0.0253 Å °0.0018 Å °0.0035 Å °-0.0106 Å °0.0453 Å °-0.0088 Å °
Refinement TLS groupSelection details: all

+
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