[English] 日本語
Yorodumi
- PDB-4xi0: MamA 41-end from Desulfovibrio magneticus RS-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xi0
TitleMamA 41-end from Desulfovibrio magneticus RS-1
ComponentsMagnetosome protein MamA
KeywordsPROTEIN BINDING / Magnetosome associated protein / protein-protein interaction / TPR motif
Function / homology
Function and homology information


: / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...: / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Magnetosome protein MamA
Similarity search - Component
Biological speciesDesulfovibrio magneticus RS-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsZarivach, R. / Zeytuni, N. / Cronin, S. / Davidov, G. / Baran, D. / Stein, T.
CitationJournal: Plos One / Year: 2015
Title: MamA as a Model Protein for Structure-Based Insight into the Evolutionary Origins of Magnetotactic Bacteria.
Authors: Zeytuni, N. / Cronin, S. / Lefevre, C.T. / Arnoux, P. / Baran, D. / Shtein, Z. / Davidov, G. / Zarivach, R.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Magnetosome protein MamA
B: Magnetosome protein MamA
C: Magnetosome protein MamA
D: Magnetosome protein MamA
E: Magnetosome protein MamA
F: Magnetosome protein MamA


Theoretical massNumber of molelcules
Total (without water)139,6716
Polymers139,6716
Non-polymers00
Water00
1
A: Magnetosome protein MamA
D: Magnetosome protein MamA
E: Magnetosome protein MamA


Theoretical massNumber of molelcules
Total (without water)69,8363
Polymers69,8363
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Magnetosome protein MamA
C: Magnetosome protein MamA
F: Magnetosome protein MamA


Theoretical massNumber of molelcules
Total (without water)69,8363
Polymers69,8363
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.087, 151.087, 204.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A41 - 214
2111B41 - 214
3111C41 - 214
4111D41 - 214
5111E41 - 214
6111F41 - 214

-
Components

#1: Protein
Magnetosome protein MamA


Mass: 23278.578 Da / Num. of mol.: 6 / Fragment: UNP residues 41-217 / Mutation: M124I, E140A, K141A, E143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio magneticus RS-1 (bacteria)
Gene: mamA, DMR_41160 / Plasmid: pET52b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: C4XPQ7

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.77 Å3/Da / Density % sol: 74.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.1 M Tris pH 8.1, 0.75 M sodium potassium tartrate and 0.5% polyethylene glycol monomethyl ether 5000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.88→22 Å / Num. obs: 51648 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.065 / Χ2: 2.455 / Net I/av σ(I): 43.89 / Net I/σ(I): 20.4 / Num. measured all: 320120
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.88-2.936.30.60825871.842100
2.93-2.986.30.47325581.662100
2.98-3.046.30.39725981.832100
3.04-3.16.30.34625711.768100
3.1-3.176.40.27425781.801100
3.17-3.246.40.20625891.82100
3.24-3.326.40.1625791.998100
3.32-3.416.40.12525812.071100
3.41-3.516.30.09925942.166100
3.51-3.636.30.08925852.214100
3.63-3.756.30.07825612.502100
3.75-3.96.30.06725972.561100
3.9-4.086.30.05525772.718100
4.08-4.296.20.05225732.856100
4.29-4.566.20.0526112.97899.9
4.56-4.916.10.05225943.341100
4.91-5.45.80.05425913.616100
5.4-6.165.80.05625943.685100
6.16-7.715.80.04326013.20599.9
7.71-225.60.03925292.90296.1

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AS5

3as5


Resolution: 2.88→22 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.2127 / FOM work R set: 0.8408 / SU B: 24.563 / SU ML: 0.207 / SU R Cruickshank DPI: 0.4661 / SU Rfree: 0.2697 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.466 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 2629 5.1 %RANDOM
Rwork0.2094 48951 --
obs0.2099 51648 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 163.97 Å2 / Biso mean: 67.091 Å2 / Biso min: 29.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.33 Å2
Refinement stepCycle: final / Resolution: 2.88→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8530 0 0 0 8530
Num. residues----1058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0228698
X-RAY DIFFRACTIONr_bond_other_d0.0030.026140
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.97511701
X-RAY DIFFRACTIONr_angle_other_deg1.145314906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68151052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18623.735431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.224151622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0671572
X-RAY DIFFRACTIONr_chiral_restr0.1040.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219622
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021760
X-RAY DIFFRACTIONr_mcbond_it1.4591.55272
X-RAY DIFFRACTIONr_mcbond_other0.2481.52122
X-RAY DIFFRACTIONr_mcangle_it3.06328386
X-RAY DIFFRACTIONr_scbond_it4.35133426
X-RAY DIFFRACTIONr_scangle_it7.8534.53315
Refine LS restraints NCS

Ens-ID: 1 / Number: 2403 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.070.05
2BTIGHT POSITIONAL0.060.05
3CTIGHT POSITIONAL0.060.05
4DTIGHT POSITIONAL0.070.05
5ETIGHT POSITIONAL0.050.05
6FTIGHT POSITIONAL0.050.05
1ATIGHT THERMAL0.160.5
2BTIGHT THERMAL0.130.5
3CTIGHT THERMAL0.10.5
4DTIGHT THERMAL0.10.5
5ETIGHT THERMAL0.110.5
6FTIGHT THERMAL0.110.5
LS refinement shellResolution: 2.879→2.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 205 -
Rwork0.356 3640 -
all-3845 -
obs--99.07 %
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)
10.19440.14480.5660.74520.42331.73540.01710.0121-0.0347-0.28320.0621-0.3268-0.0661-0.0601-0.07920.17760.02760.11230.18410.03920.201446.446647.909284.1337
20.35050.53140.32841.65560.28510.36380.0831-0.1595-0.05290.1189-0.020.0530.0527-0.2047-0.06310.136-0.0150.04230.23760.11450.179431.094331.4398105.9765
31.1138-0.87080.8410.8834-0.48510.7829-0.08530.06580.10830.02480.0465-0.1572-0.11510.12510.03880.3105-0.08640.12070.13330.01960.333139.8913-7.3822101.6774
40.6833-0.75150.31093.08560.0770.2212-0.03830.06420.15020.2912-0.09270.28360.01040.01650.13090.5663-0.04030.14430.30540.03690.22821.00556.260254.2411
50.7989-0.77830.74281.1692-0.39640.95740.10790.0681-0.1779-0.0603-0.11010.34990.08460.00780.00220.2419-0.10180.04110.1955-0.05770.4632.219584.924379.9583
60.6607-0.69710.2843.91890.09220.18870.04530.127-0.0688-0.04950.0238-0.4723-0.03550.002-0.06910.5658-0.02220.19290.3398-0.08140.207456.010213.5758131.8801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999

+
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