[English] 日本語
Yorodumi
- PDB-9m3b: Crystal structure of the DgpB1/C1 protein from P581a substrate fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9m3b
TitleCrystal structure of the DgpB1/C1 protein from P581a substrate free form
Components
  • P581a DgpB1
  • P581a DgpC1
KeywordsISOMERASE / C-glycoside isomerase / homoorientin / human gut microbiota
Function / homology:
Function and homology information
Biological specieshuman gut metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.036 Å
AuthorsMa, W.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Crystal structure of W974-1 DgpA1 structure
Authors: Ma, W.
History
DepositionMar 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P581a DgpC1
B: P581a DgpB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7553
Polymers53,7002
Non-polymers551
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-13 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.188, 58.873, 56.931
Angle α, β, γ (deg.)90.00, 97.97, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein P581a DgpC1


Mass: 38811.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human gut metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Protein P581a DgpB1


Mass: 14888.935 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human gut metagenome (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium malonate, pH 6.0 12% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33683 / % possible obs: 94.8 % / Redundancy: 6 % / CC1/2: 0.79 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 2307 / CC1/2: 0.78

-
Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.036→43.946 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 2000 5.94 %
Rwork0.1915 --
obs0.1929 33683 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.036→43.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 0 1 196 3922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073842
X-RAY DIFFRACTIONf_angle_d0.8265222
X-RAY DIFFRACTIONf_dihedral_angle_d3.2382304
X-RAY DIFFRACTIONf_chiral_restr0.052586
X-RAY DIFFRACTIONf_plane_restr0.005671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.036-2.08640.3252740.2721174X-RAY DIFFRACTION50
2.0864-2.14280.24591490.20532365X-RAY DIFFRACTION99
2.1428-2.20590.2421500.20062364X-RAY DIFFRACTION100
2.2059-2.27710.25691490.19432380X-RAY DIFFRACTION100
2.2771-2.35850.22531500.19612355X-RAY DIFFRACTION99
2.3585-2.45290.22621470.19452344X-RAY DIFFRACTION100
2.4529-2.56450.24611510.19342396X-RAY DIFFRACTION99
2.5645-2.69970.23891490.19562359X-RAY DIFFRACTION99
2.6997-2.86880.22291490.19792343X-RAY DIFFRACTION99
2.8688-3.09030.21191480.20082368X-RAY DIFFRACTION99
3.0903-3.40120.23351500.19592368X-RAY DIFFRACTION99
3.4012-3.89310.18681360.18262147X-RAY DIFFRACTION91
3.8931-4.90380.2041440.17832288X-RAY DIFFRACTION98
4.9038-43.9460.19321540.18912432X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 23.4576 Å / Origin y: 6.1595 Å / Origin z: 4.2873 Å
111213212223313233
T0.2089 Å2-0.0072 Å20.0076 Å2-0.208 Å20.0139 Å2--0.2225 Å2
L1.052 °20.0997 °20.0951 °2-0.3847 °2-0.071 °2--0.8117 °2
S-0.0162 Å °0.0628 Å °0.1253 Å °-0.012 Å °0.0357 Å °0.141 Å °-0.0015 Å °-0.1535 Å °-0.0065 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