[English] 日本語
Yorodumi
- PDB-9p4u: Nucleotide Binding Domain (residues 475-720) of ABC3 transporter ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9p4u
TitleNucleotide Binding Domain (residues 475-720) of ABC3 transporter permease from Clostridioides difficile strain 630
ComponentsABC-type transport system, permease protein
KeywordsTRANSPORT PROTEIN / Center for Structural Biology of Infectious Diseases / CSBID / ABC-type transport system / Nucleotide Binding Domain / Structural Genomics
Function / homology: / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / transmembrane transporter activity / plasma membrane / ABC-type transport system, permease protein
Function and homology information
Biological speciesClostridioides difficile 630 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Wawrzak, Z. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: To Be Published
Title: Nucleotide Binding Domain (residues 475-720) of ABC3 transporter permease from Clostridioides difficile strain 630
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Wawrzak, Z. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases
History
DepositionJun 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC-type transport system, permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6838
Polymers28,4201
Non-polymers2647
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.352, 79.828, 88.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ABC-type transport system, permease protein


Mass: 28419.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile 630 (bacteria)
Strain: 630 / Gene: CD630_14670 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q18BY6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein: 7.6mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: PACT (B10), 0.2M Magnesium chloride, 0.1M MES (pH 6.0), 20% (w/v) PEG6000 Cryo: drop conditions

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97895 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 15239 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 25.1 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.067 / Rrim(I) all: 0.193 / Rsym value: 0.181 / Χ2: 1.048 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 761 / CC1/2: 0.731 / CC star: 0.919 / Rpim(I) all: 0.341 / Χ2: 1.006 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.62 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.049 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 771 5.1 %RANDOM
Rwork0.1966 ---
obs0.199 14374 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.69 Å2 / Biso mean: 33.853 Å2 / Biso min: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å20 Å2
2--1.79 Å20 Å2
3---1.82 Å2
Refinement stepCycle: final / Resolution: 2→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 11 110 1916
Biso mean--50.5 34.37 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131820
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161776
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.6432440
X-RAY DIFFRACTIONr_angle_other_deg0.3721.5954097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6655222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.51324.94999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.92515357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.661157
X-RAY DIFFRACTIONr_chiral_restr0.0670.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0560.022063
X-RAY DIFFRACTIONr_gen_planes_other0.0490.02407
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.319 43 -
Rwork0.288 1061 -
obs--100 %

+
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