[English] 日本語
Yorodumi
- PDB-9c8w: X-ray crystal structure of Methylorubrum extorquens apo LanD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c8w
TitleX-ray crystal structure of Methylorubrum extorquens apo LanD
Componentslandiscernin
KeywordsMETAL BINDING PROTEIN / lanthanide / chaperone / methanol dehydrogenase / metal-centered dimer
Function / homologyHistidine kinase
Function and homology information
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJung, J.J. / Lin, C.-Y. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Modulating metal-centered dimerization of a lanthanide chaperone protein for separation of light lanthanides.
Authors: Larrinaga, W.B. / Jung, J.J. / Lin, C.Y. / Boal, A.K. / Cotruvo Jr., J.A.
History
DepositionJun 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: landiscernin
B: landiscernin


Theoretical massNumber of molelcules
Total (without water)13,2052
Polymers13,2052
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-1 kcal/mol
Surface area7580 Å2
Unit cell
Length a, b, c (Å)76.776, 23.507, 76.446
Angle α, β, γ (deg.)90.00, 120.02, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein landiscernin


Mass: 6602.546 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (bacteria) / Gene: LanD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5B159
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium fluoride, 20% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.65→38.39 Å / Num. obs: 21758 / % possible obs: 96.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 13.29 Å2 / CC1/2: 1 / Net I/σ(I): 28.4
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 1073 / CC1/2: 0.9

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→38.39 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1070 4.92 %
Rwork0.2119 --
obs0.2141 21758 78.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 0 186 1075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.816
X-RAY DIFFRACTIONf_dihedral_angle_d12.071357
X-RAY DIFFRACTIONf_chiral_restr0.042134
X-RAY DIFFRACTIONf_plane_restr0.007164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.730.3208700.25351340X-RAY DIFFRACTION40
1.73-1.820.2941900.26891724X-RAY DIFFRACTION52
1.82-1.930.24541140.24152031X-RAY DIFFRACTION63
1.93-2.080.24251360.21882660X-RAY DIFFRACTION80
2.08-2.290.24711670.19873149X-RAY DIFFRACTION96
2.29-2.620.28061640.21233310X-RAY DIFFRACTION100
2.62-3.310.28521760.21413276X-RAY DIFFRACTION99
3.31-38.390.22361530.19883198X-RAY DIFFRACTION97
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)
10.98791.09011.20892.8620.64542.93030.1082-0.8058-0.31960.8439-0.17570.28180.45-0.4124-0.32920.44580.01790.15710.48280.1780.32862.03530.414328.011
24.69952.59410.02614.5598-0.19432.10330.0857-0.28480.03250.1487-0.1226-0.1620.0108-0.13170.04540.0620.00020.00130.07030.03010.062412.1428.900212.9986
34.31251.91350.6613.43390.00482.54-0.14630.42250.0975-0.31010.1256-0.1253-0.16050.06870.04570.10840.00910.04430.08150.03890.066412.46498.23442.0255
45.45771.05752.5172.2740.35694.30430.07160.0634-0.0437-0-0.0893-0.41930.29060.0901-0.08810.09350.01120.01240.07210.0280.148915.56281.96457.1547
56.1283-1.43611.13663.6645-0.05772.1549-0.2917-0.1509-0.22310.2766-0.06990.37520.0991-0.3160.06050.1373-0.00730.04920.2347-0.00250.10941.03296.250119.9628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 58 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 91 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 57 )

+
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