[English] 日本語
Yorodumi
- PDB-7mmx: CutN from Type I Cut MCP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mmx
TitleCutN from Type I Cut MCP
ComponentsPropanediol utilization protein PduA
KeywordsSTRUCTURAL PROTEIN / microcompartment / MCP / shell protein / Cut MCP / choline utilization
Function / homologybacterial microcompartment / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Propanediol utilization protein PduA
Function and homology information
Biological speciesStreptococcus intermedius SK54 = ATCC 27335 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsOchoa, J.M. / 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
DepositionApr 30, 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: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
C: Propanediol utilization protein PduA
D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,94310
Polymers61,5596
Non-polymers3844
Water3,081171
1
A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
C: Propanediol utilization protein PduA
hetero molecules

A: Propanediol utilization protein PduA
B: Propanediol utilization protein PduA
C: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,13512
Polymers61,5596
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10930 Å2
ΔGint-149 kcal/mol
Surface area19340 Å2
MethodPISA
2
D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
hetero molecules

D: Propanediol utilization protein PduA
E: Propanediol utilization protein PduA
F: Propanediol utilization protein PduA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7518
Polymers61,5596
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10650 Å2
ΔGint-136 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.500, 49.660, 92.410
Angle α, β, γ (deg.)90.000, 93.830, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-101-

SO4

-
Components

#1: Protein
Propanediol utilization protein PduA


Mass: 10259.764 Da / Num. of mol.: 6 / Fragment: BMC domain, residues 1-92 / Mutation: K27D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius SK54 = ATCC 27335 (bacteria)
Gene: HMPREF1654_00408 / Plasmid: plasmid / Details (production host): pET-24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0E2J8H5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 1.26 M Ammonium sulfate, 0.1 M HEPES/ Sodium hydroxide pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→92.2 Å / Num. obs: 38026 / % possible obs: 98.5 % / Redundancy: 6.574 % / Biso Wilson estimate: 30.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.078 / Χ2: 0.991 / Net I/σ(I): 14.97 / Num. measured all: 249994 / Scaling rejects: 189
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
1.9-1.954.8510.7092.2512085279824910.8430.79489
1.95-26.1330.523.6816315275526600.9460.56896.6
2-2.066.7760.4185.0818200269926860.9610.45399.5
2.06-2.126.760.3466.1217663262126130.9630.37599.7
2.12-2.196.5620.2946.9216588253525280.9680.3299.7
2.19-2.276.8620.2627.9616804245624490.9750.28499.7
2.27-2.366.890.2059.7316239237123570.9850.22299.4
2.36-2.456.6750.15811.6715079227722590.9910.17199.2
2.45-2.566.3260.1412.2113741220921720.9910.15398.3
2.56-2.697.0760.1214.9114584206420610.9950.12999.9
2.69-2.837.0420.1021713999199719880.9960.1199.5
2.83-36.8150.08319.2412785187818760.9960.0999.9
3-3.216.9280.06723.3712270178117710.9970.07399.4
3.21-3.476.5750.05827.2410947167116650.9970.06399.6
3.47-3.86.160.04829.99240152415000.9980.05398.4
3.8-4.257.0410.04236.099815139813940.9980.04699.7
4.25-4.916.8380.0436.658411123912300.9980.04499.3
4.91-6.016.8320.04235.387051103710320.9980.04599.5
6.01-8.56.2620.04236.0951728318260.9990.04699.4
8.5-92.26.4230.0437.3230064684680.9990.043100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å92.2 Å
Translation1.9 Å92.2 Å

-
Processing

Software
NameVersionClassification
BUSTERrefinement
XSCALEdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AXJ

4axj


Resolution: 1.9→92.2 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.164 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 3803 10 %RANDOM
Rwork0.212 ---
obs0.2144 38026 98.4 %-
Displacement parametersBiso max: 77.9 Å2 / Biso mean: 33.41 Å2 / Biso min: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1-4.6262 Å20 Å22.1379 Å2
2---6.5185 Å20 Å2
3---1.8922 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.9→92.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 20 171 3798
Biso mean--51.23 39.93 -
Num. residues----522
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1206SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes623HARMONIC5
X-RAY DIFFRACTIONt_it3653HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion521SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance20HARMONIC1
X-RAY DIFFRACTIONt_utility_angle7HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3384SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3653HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4974HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion15.5
LS refinement shellResolution: 1.9→1.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3384 76 9.99 %
Rwork0.3258 685 -
all0.3272 761 -
obs--83.46 %
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)
12.10480.11340.30850.34180.38460.5985-0.02060.02480.02390.040.025-0.0084-0.01610.0378-0.00440.00490.0002-0.019-0.0292-0.0044-0.01713.900713.723921.4338
22.12950.14352.31210.16520.07243.10040.05830.05340.08330.0046-0.01090.0599-0.0398-0.0154-0.0473-0.03530.00260.0129-0.0130.0094-0.0441-16.404814.716313.6133
31.1502-0.314-0.76740.4707-0.04861.925-0.0587-0.1074-0.022-0.0350.05490.0199-0.06690.08970.0038-0.020.0114-0.0221-0.0192-0.0016-0.017-21.312214.3505-6.8089
42.4483-0.36120.92410.226-0.4981.7275-0.0417-0.12440.032-0.03580.04840.0187-0.0841-0.0727-0.0067-0.00320.0111-0.0147-0.0277-0.0033-0.0233-8.4448-11.115924.9374
52.8008-0.25371.10790.2113-0.27082.68940.089-0.15550.2126-0.0643-0.03310.02420.01090.223-0.0558-0.0563-0.00880.02160.0236-0.0276-0.064612.2402-10.403330.7646
62.02710.9306-0.18360.32850.03763.6942-0.09430.2886-0.14660.13320.11480.0066-0.05970.2723-0.0205-0.1053-0.0182-0.00910.1114-0.0313-0.08617.6657-10.974752.0077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 89
2X-RAY DIFFRACTION2{ B|* }B5 - 92
3X-RAY DIFFRACTION3{ C|* }C-3 - 89
4X-RAY DIFFRACTION4{ D|* }D4 - 89
5X-RAY DIFFRACTION5{ E|* }E4 - 90
6X-RAY DIFFRACTION6{ F|* }F5 - 89

+
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