[English] 日本語
Yorodumi
- PDB-4nps: Crystal Structure of Bep1 protein (VirB-translocated Bartonella e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nps
TitleCrystal Structure of Bep1 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae
ComponentsBartonella effector protein (Bep) substrate of VirB T4SS
KeywordsCELL ADHESION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / FIC domain
Function / homology
Function and homology information


protein adenylyltransferase
Similarity search - Function
BepA, intracellular delivery domain / Intracellular delivery domain / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...BepA, intracellular delivery domain / Intracellular delivery domain / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / protein adenylyltransferase
Similarity search - Component
Biological speciesBartonella clarridgeiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsDranow, D.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Microorganisms / Year: 2021
Title: Evolutionary Diversification of Host-Targeted Bartonella Effectors Proteins Derived from a Conserved FicTA Toxin-Antitoxin Module.
Authors: Schirmer, T. / de Beer, T.A.P. / Tamegger, S. / Harms, A. / Dietz, N. / Dranow, D.M. / Edwards, T.E. / Myler, P.J. / Phan, I. / Dehio, C.
History
DepositionNov 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 8, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _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
Revision 1.3Aug 24, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Sep 20, 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: Bartonella effector protein (Bep) substrate of VirB T4SS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9423
Polymers63,8241
Non-polymers1182
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.190, 97.850, 49.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Bartonella effector protein (Bep) substrate of VirB T4SS


Mass: 63824.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella clarridgeiae (bacteria) / Strain: CIP 104772 / 73 / Gene: BARCL_0069 / Production host: Escherichia coli (E. coli) / References: UniProt: E6YFW2
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus(g5): 10% PEG-20,000, 20% PEG MME 550, 0.1M MOPS/HEPES-Na, pH=7.5, 0.02M each Sodium Formate, Ammonium Acetate, Trisodium Citrate, Sodium Potassium L-Tartrate, Sodium Oxamate, VAPOR ...Details: Morpheus(g5): 10% PEG-20,000, 20% PEG MME 550, 0.1M MOPS/HEPES-Na, pH=7.5, 0.02M each Sodium Formate, Ammonium Acetate, Trisodium Citrate, Sodium Potassium L-Tartrate, Sodium Oxamate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→58.61 Å / Num. all: 28535 / Num. obs: 28414 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 36.969 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 27.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.950.5223.710900206599.7
1.95-20.3894.7310664203399.8
2-2.060.2886.4210418196799.8
2.06-2.120.2128.4310064190499.7
2.12-2.190.15810.99679183999.7
2.19-2.270.12313.619547182099.8
2.27-2.360.10116.289125173599.9
2.36-2.450.08419.018817168499.8
2.45-2.560.06423.868274157799.8
2.56-2.690.05327.817991153899.7
2.69-2.830.04332.87641146599.9
2.83-30.03439.897246140099.7
3-3.210.02945.686730132899.9
3.21-3.470.02454.326133122199.6
3.47-3.80.02161.95540112999.6
3.8-4.250.01967.335055103699.5
4.25-4.910.01772.74456493799.3
4.91-6.010.01869.78373477199.6
6.01-8.50.01768.74290362499.4
8.50.01667.27133234188.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JK8

2jk8


Resolution: 1.9→58.61 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2116 / WRfactor Rwork: 0.1683 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8659 / SU B: 5.513 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1217 / SU Rfree: 0.1213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY. RESIDUES 313-558 ARE MISSING IN THE ELECTRON DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 1435 5.1 %RANDOM
Rwork0.1717 ---
all0.1737 29849 --
obs0.1737 28414 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.68 Å2 / Biso mean: 35.176 Å2 / Biso min: 11.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å2-0 Å2
2---0.81 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→58.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 8 161 2332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192238
X-RAY DIFFRACTIONr_bond_other_d0.0010.022086
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.963041
X-RAY DIFFRACTIONr_angle_other_deg0.84634810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3295289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21425.55699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46315377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.947156
X-RAY DIFFRACTIONr_chiral_restr0.090.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
X-RAY DIFFRACTIONr_mcbond_it1.4081.8721137
X-RAY DIFFRACTIONr_mcbond_other1.3771.8621134
X-RAY DIFFRACTIONr_mcangle_it1.9832.7811419
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 114 -
Rwork0.23 1946 -
all-2060 -
obs--99.57 %
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)
11.1117-0.34390.43694.2719-1.00581.43540.030.0215-0.0348-0.2779-0.01790.18710.0211-0.1452-0.01210.10410.0208-0.01920.08960.00660.137256.15215.951912.6433
22.22431.1610.00572.67870.42311.42290.0612-0.27940.05050.1086-0.04290.0488-0.0858-0.0671-0.01830.10040.04510.03660.1131-0.02160.127563.450316.195824.4576
31.97370.3011-0.54661.5508-0.60341.9604-0.0820.08140.1071-0.19080.09880.0112-0.02720.0381-0.01680.145-0.0290.01360.0675-0.01950.108586.10420.95837.6109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 64
2X-RAY DIFFRACTION2A65 - 191
3X-RAY DIFFRACTION3A192 - 312

+
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