[English] 日本語
Yorodumi
- PDB-5sv6: Crystal structure of MxaJ from Methlophaga aminisulfidivorans MPT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5sv6
TitleCrystal structure of MxaJ from Methlophaga aminisulfidivorans MPT
ComponentsExtracellular solute-binding protein, family 3
KeywordsUNKNOWN FUNCTION / MxaJ / Methlophaga aminisulfidivorans / MDH / PBP
Function / homologymethanol catabolic process / Methanol oxidation system protein MoxJ / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / periplasmic space / BROMIDE ION / Extracellular solute-binding protein, family 3
Function and homology information
Biological speciesMethylophaga aminisulfidivorans MP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsChoi, J.M. / Lee, S.H.
CitationJournal: Proteins / Year: 2017
Title: MxaJ structure reveals a periplasmic binding protein-like architecture with unique secondary structural elements
Authors: Choi, J.M. / Cao, T.P. / Kim, S.W. / Lee, K.H. / Lee, S.H.
History
DepositionAug 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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
A: Extracellular solute-binding protein, family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9202
Polymers32,8401
Non-polymers801
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.127, 63.761, 99.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Extracellular solute-binding protein, family 3 / MxaJ


Mass: 32839.879 Da / Num. of mol.: 1 / Fragment: UNP residues 12-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophaga aminisulfidivorans MP (bacteria)
Strain: MP / Gene: mxaJ / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A3FJ49
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 1.79 Å3/Da / Density % sol: 31.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M sodium bromide, 20%(w/v) PEG 3350, 10%(w/v) glycerol, 0.1M Tris HCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2010
RadiationMonochromator: DCM Si(111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 18684 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 0.69
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 16.049 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.92→29.728 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.33 / Phase error: 21.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 1848 10.17 %Random
Rwork0.1779 ---
obs0.1841 18174 97.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→29.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 1 285 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071980
X-RAY DIFFRACTIONf_angle_d1.042677
X-RAY DIFFRACTIONf_dihedral_angle_d13.148755
X-RAY DIFFRACTIONf_chiral_restr0.077296
X-RAY DIFFRACTIONf_plane_restr0.005347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9193-1.97120.2481310.15961119X-RAY DIFFRACTION88
1.9712-2.02920.23621400.15671183X-RAY DIFFRACTION94
2.0292-2.09470.21711390.15731211X-RAY DIFFRACTION96
2.0947-2.16950.22411420.15411239X-RAY DIFFRACTION96
2.1695-2.25630.26161390.15721212X-RAY DIFFRACTION96
2.2563-2.3590.22571390.16011242X-RAY DIFFRACTION97
2.359-2.48330.23261440.18921261X-RAY DIFFRACTION98
2.4833-2.63880.22641410.18541267X-RAY DIFFRACTION99
2.6388-2.84240.25791420.19091286X-RAY DIFFRACTION99
2.8424-3.12810.28241420.19751281X-RAY DIFFRACTION99
3.1281-3.58010.22331460.17951302X-RAY DIFFRACTION100
3.5801-4.50810.21151470.17161327X-RAY DIFFRACTION100
4.5081-29.73110.26111560.19311396X-RAY DIFFRACTION99

+
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