[English] 日本語
Yorodumi
- PDB-3s03: The crystal structure of the periplasmic domain of Helicobacter p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s03
TitleThe crystal structure of the periplasmic domain of Helicobacter pylori MotB (residues 97-256, P43).
ComponentsMotility protein B
KeywordsMOTOR PROTEIN / peptidoglycan binding / flagellar rotation / chemotaxis / bacterial flagellar motor / membrane
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / chemotaxis / identical protein binding / plasma membrane
Similarity search - Function
Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / OmpA-like domain / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRoujeinikova, A.R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Role of the MotB linker in the assembly and activation of the bacterial flagellar motor.
Authors: O'Neill, J. / Xie, M. / Hijnen, M. / Roujeinikova, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Cloning, purification and crystallization of MotB, a stator component of the proton-driven bacterial flagellar motor.
Authors: O'Neill, J. / Roujeinikova, A.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Motility protein B
B: Motility protein B
C: Motility protein B
D: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,17811
Polymers75,5064
Non-polymers6727
Water2,612145
1
A: Motility protein B
D: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9454
Polymers37,7532
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-43 kcal/mol
Surface area15210 Å2
MethodPISA
2
B: Motility protein B
C: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2337
Polymers37,7532
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-84 kcal/mol
Surface area15100 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-143 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.669, 71.669, 126.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein
Motility protein B / Chemotaxis protein MotB


Mass: 18876.377 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN (UNP Residues 98-257)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0816, motB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P56427
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM citric acid pH 5.0, 0.8 M Ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→71.67 Å / Num. all: 18607 / Num. obs: 18607 / % possible obs: 85 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.643.40.3192.4955628160.31987.7
2.64-2.83.40.2443.1906226380.24487.2
2.8-2.993.40.1864836224470.18686.5
2.99-3.233.50.1484.7796122830.14886.5
3.23-3.543.50.1275.2723820560.12785.1
3.54-3.953.50.1146659118600.11484.4
3.95-4.563.60.1066.1574616010.10682.8
4.56-5.593.70.0887.5496113560.08882.1
5.59-7.913.70.0778.3382210250.07780.3
7.91-71.6113.80.069.919725250.0674.7

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.1data scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→71.67 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.386 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2843 981 5.3 %RANDOM
Rwork0.2251 ---
obs0.2281 18571 84.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 113.46 Å2 / Biso mean: 50.13 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20 Å2
2--1.37 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→71.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 35 145 4664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224593
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9656215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5935556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.88124.825228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63715817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3851529
X-RAY DIFFRACTIONr_chiral_restr0.0760.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213461
X-RAY DIFFRACTIONr_mcbond_it5.5051.52814
X-RAY DIFFRACTIONr_mcangle_it7.40724563
X-RAY DIFFRACTIONr_scbond_it9.16631779
X-RAY DIFFRACTIONr_scangle_it10.8014.51652
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 90 -
Rwork0.38 1327 -
all-1417 -
obs--86.51 %
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)
10.3294-0.03410.05080.25160.07860.0395-0.02110.0386-0.01970.06390.00220.0399-0.00170.01040.0190.14190.0034-0.0070.15130.02850.034110.6770.738-8.96
20.23580.03360.01360.56950.34690.32780.01610.0188-0.05980.015-0.014-0.0274-0.01130.0359-0.0020.12750.0107-0.00750.14810.01070.034821.207-9.741-6.41
30.59630.0177-0.01421.1929-0.4080.1457-0.0669-0.08030.11710.08420.0627-0.0767-0.0009-0.01650.00430.14920.0091-0.07340.0994-0.02810.052331.30825.1228.563
40.8278-0.00240.10610.61150.1450.0575-0.0298-0.00110.01690.0680.0465-0.1301-0.0149-0.0146-0.01670.18830.0049-0.0770.11090.00170.050442.87115.1978.903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A106 - 250
2X-RAY DIFFRACTION2B106 - 251
3X-RAY DIFFRACTION3C106 - 251
4X-RAY DIFFRACTION4D103 - 251

+
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