[English] 日本語
Yorodumi
- PDB-7mpw: CmcB from Type II Cut MCP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mpw
TitleCmcB from Type II Cut MCP
ComponentsBMC domain-containing protein
KeywordsSTRUCTURAL PROTEIN / microcompartment / MCP / shell protein / Cut MCP / choline utilization
Function / homology
Function and homology information


ethanolamine catabolic process / bacterial microcompartment
Similarity search - Function
CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
Similarity search - Domain/homology
BMC domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MAD / molecular replacement / Resolution: 3.001 Å
AuthorsOchoa, J.M. / Marshall, J.D. / Sawaya, M.R. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments
Authors: Ochoa, J.M. / Mijares, O. / Acosta, A.A. / Escoto, X. / Leon-Rivera, N. / Marshall, J.D. / Sawaya, M.R. / Yeates, T.O.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BMC domain-containing protein
B: BMC domain-containing protein
C: BMC domain-containing protein
D: BMC domain-containing protein
E: BMC domain-containing protein
F: BMC domain-containing protein


Theoretical massNumber of molelcules
Total (without water)63,6616
Polymers63,6616
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, CmcB elutes as a hexamer. The elution profile is consistent with a predicted molecular mass of approximately 62 KDa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-72 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.230, 52.400, 61.160
Angle α, β, γ (deg.)107.420, 96.580, 101.960
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
BMC domain-containing protein / Propanediol utilization protein PduA / Propanediol utilization protein pduA/pduJ / Putative ...Propanediol utilization protein PduA / Propanediol utilization protein pduA/pduJ / Putative Propanediol utilization protein pduA/pduJ


Mass: 10610.086 Da / Num. of mol.: 6 / Mutation: K25D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pduA_2 / Plasmid: pET-24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8G9V6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 294 K / Method: vapor diffusion
Details: 1.0 M Sodium acetate trihydrate, 0.1 M Imidazole pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→57.3 Å / Num. obs: 8055 / % possible obs: 97.1 % / Redundancy: 3.86 % / Biso Wilson estimate: 69.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.108 / Χ2: 0.882 / Net I/σ(I): 12.3 / Num. measured all: 31090 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.083.6830.6022.3221626495870.8490.70290.4
3.08-3.163.8940.5322.8321965795640.8740.61797.4
3.16-3.253.9170.3953.7422525965750.9250.45796.5
3.25-3.353.8920.3144.5921175625440.9580.36496.8
3.35-3.463.9020.2386.0119865275090.970.27696.6
3.46-3.593.890.178.0421165525440.9840.19798.6
3.59-3.723.8930.1459.1518925044860.990.16896.4
3.72-3.873.8990.1499.0518094754640.9890.17397.7
3.87-4.053.8930.11811.3318574904770.990.13797.3
4.05-4.243.8780.07215.2516254244190.9980.08498.8
4.24-4.473.8780.06219.2616564404270.9970.07197
4.47-4.743.8660.05820.8215314073960.9970.06897.3
4.74-5.073.8920.06319.4914093653620.9960.07399.2
5.07-5.483.810.06218.9513033483420.9960.07298.3
5.48-63.8620.09413.4812863373330.9930.10998.8
6-6.713.8660.06618.1811252962910.9960.07798.3
6.71-7.753.8310.04524.389962632600.9980.05298.9
7.75-9.493.7280.02735.958092202170.9990.03298.6
9.49-13.423.8220.02937.5964617116910.03498.8
13.42-57.33.5620.02737.0331791890.9990.03297.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å42.86 Å
Translation2 Å42.86 Å

-
Processing

Software
NameVersionClassification
BUSTERrefinement
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD
Starting model: 4QIV

4qiv


Resolution: 3.001→57.3 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.476
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 806 10.01 %RANDOM
Rwork0.2213 ---
obs0.2248 8055 97.4 %-
Displacement parametersBiso max: 127.03 Å2 / Biso mean: 70.1 Å2 / Biso min: 23.49 Å2
Baniso -1Baniso -2Baniso -3
1--13.2045 Å2-14.1954 Å26.2587 Å2
2---1.3455 Å2-2.3848 Å2
3---14.55 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 3.001→57.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 0 7 3327
Biso mean---34.93 -
Num. residues----485
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1113SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes589HARMONIC5
X-RAY DIFFRACTIONt_it3331HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion484SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance12HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2575SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3331HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4534HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion16.21
LS refinement shellResolution: 3.001→3.03 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2535 21 10.4 %
Rwork0.3246 181 -
obs--84.68 %
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)
14.7622-2.6621.56945.265-2.307810.54110.07470.2237-0.0556-0.3174-0.1486-0.23960.08410.2680.0739-0.07280.0858-0.0728-0.0424-0.1255-0.19584.7642-24.72697.6328
23.2455-3.90461.07675.9299-0.47579.75950.024-0.0964-0.2634-0.1963-0.0771-0.1191-0.4435-0.45620.0531-0.05250.1125-0.0613-0.053-0.1196-0.1641-8.2983-11.18917.9082
31.6064-1.97371.60615.4533-0.72097.6389-0.1733-0.2039-0.18370.25520.0860.1583-0.7101-0.86540.08730.01060.19860.05330.0549-0.1046-0.2069-6.9569-9.589939.219
48.4487-4.44941.55535.38320.64946.4581-0.4932-0.50250.28220.35390.5938-0.032-0.0069-0.2341-0.1006-0.00850.12740.0253-0.0468-0.0178-0.28238.9455-21.455550.6318
53.1197-4.6113-0.03885.02941.906510.8395-0.1085-0.27220.36170.23110.14930.24430.71450.9298-0.0408-0.04010.1081-0.0055-0.01230.0243-0.217619.446-37.692240.8733
64.1817-2.29370.10932.1026-0.41518.8577-0.00090.1199-0.22960.1150.01760.18070.70730.5594-0.01670.01060.10280.0224-0.0536-0.1252-0.161117.3223-39.845218.7708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 86
2X-RAY DIFFRACTION2{ B|* }B3 - 83
3X-RAY DIFFRACTION3{ C|* }C3 - 81
4X-RAY DIFFRACTION4{ D|* }D3 - 83
5X-RAY DIFFRACTION5{ E|* }E3 - 81
6X-RAY DIFFRACTION6{ F|* }F4 - 84

+
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://pdbjlvh1.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