[English] 日本語
Yorodumi
- PDB-4lgo: Crystal Structure of N-terminal domain 1 of VompD from Bartonella... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lgo
TitleCrystal Structure of N-terminal domain 1 of VompD from Bartonella quintana
ComponentsVompD
KeywordsCELL ADHESION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / trimeric autotransporter adhesin / autotransporter adhesin / outer membrane
Function / homology
Function and homology information


: / cell outer membrane / membrane => GO:0016020 / cell surface
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
Surface protein/Bartonella adhesin / VompD
Similarity search - Component
Biological speciesBartonella quintana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of N-terminal domain 1 of VompD from Bartonella quintana
Authors: Dranow, D.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: VompD
B: VompD
C: VompD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9955
Polymers43,8713
Non-polymers1242
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-109 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.030, 37.110, 109.780
Angle α, β, γ (deg.)90.000, 119.430, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

21B-583-

HOH

-
Components

#1: Protein VompD


Mass: 14623.595 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: Toulouse / Gene: vompD / Production host: Escherichia coli (E. coli) / References: UniProt: Q64HT0, UniProt: A0A0H3LUZ2*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: Wizard3/4_b12: 2M Ammonium Sulfate, 0.1M Sodium Acetate/HCl, pH=4.6, VAPOR DIFFUSION, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2013 / Details: beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 46989 / Num. obs: 46707 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 30.647 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 20.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.4812.7212835344699.8
1.74-1.790.3963.3112371331499.7
1.79-1.840.2774.7212249328299.8
1.84-1.90.2126.2311775315399.7
1.9-1.960.1538.4311512308199.5
1.96-2.030.11211.1111079295999.7
2.03-2.110.08614.1210689285199.7
2.11-2.190.07316.3310373276699.7
2.19-2.290.06318.699921264499.5
2.29-2.40.05321.89590256099.5
2.4-2.530.04525.258958238199.4
2.53-2.690.03929.188650230299.5
2.69-2.870.03333.568072215799
2.87-3.10.02938.797482200399.4
3.1-3.40.02444.846911185199
3.4-3.80.02249.266218167599.2
3.8-4.390.02151.315485148098.7
4.39-5.380.0253.944657127098.3
5.38-7.60.0252.253594100698.8
7.60.01853.02175552689.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D9X

3d9x


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.512 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 2364 5.1 %RANDOM
Rwork0.1668 ---
all0.1679 46989 --
obs0.1679 46707 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.35 Å2 / Biso mean: 30.409 Å2 / Biso min: 7.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-0.44 Å2
2--2.71 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 8 281 2870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192630
X-RAY DIFFRACTIONr_bond_other_d0.0010.022596
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9353562
X-RAY DIFFRACTIONr_angle_other_deg0.73635936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.78827.686121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37115454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.898158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
X-RAY DIFFRACTIONr_mcbond_it1.1181.4521417
X-RAY DIFFRACTIONr_mcbond_other1.1181.451416
X-RAY DIFFRACTIONr_mcangle_it1.8752.1631768
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 166 -
Rwork0.258 3270 -
all-3436 -
obs--99.85 %
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)
11.5927-0.17910.45870.6320.30044.01530.1295-0.3410.1869-0.01070.07170.0249-0.4342-0.5393-0.20120.08860.04690.03720.1456-0.0140.141816.938812.844861.3039
20.4782-0.2031-0.81970.2355-0.15544.49690.03420.0582-0.03-0.06490.0130.09410.2076-0.146-0.04710.0835-0.0178-0.02520.0398-0.00210.126926.13884.722631.8344
31.19111.1529-1.57554.82563.22098.2202-0.02150.1335-0.039-0.30760.0191-0.1005-0.198-0.29460.00240.21160.0719-0.03150.10870.00270.085930.52987.40132.953
41.71080.03081.64762.587-1.983523.31570.2511-0.3444-0.21910.21030.35040.13930.7768-1.3286-0.60150.0885-0.0945-0.01010.47170.09710.16594.74642.339965.8048
50.6508-0.0785-0.37490.1138-0.01753.9930.02660.0155-0.0238-0.02570.03940.02320.2462-0.3664-0.0660.0696-0.0177-0.02950.0496-0.00130.134922.93773.771140.8003
61.23490.146-0.10175.7532-4.45639.48520.02010.3538-0.0857-0.36170.0547-0.0670.14920.3536-0.07480.10740.0434-0.00120.1821-0.01790.02238.01867.55915.1752
75.72610.2093-1.88935.471-0.984310.79130.0845-0.62960.24440.10460.15720.2503-0.698-0.5104-0.24170.12640.1440.05510.2874-0.02440.189610.998118.680564.3544
81.51340.0705-0.29850.2924-0.52274.69760.1308-0.06910.04480.00590.18420.10310.0475-0.916-0.3150.0178-0.0151-0.00960.22250.06960.121412.08256.059248.9107
91.66670.11640.05961.16430.8954.09080.0480.3169-0.0453-0.1338-0.00690.03490.24080.1478-0.04110.11580.0288-0.02570.0854-0.00330.0532.33034.261813.508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A223 - 268
2X-RAY DIFFRACTION2A269 - 321
3X-RAY DIFFRACTION3A322 - 339
4X-RAY DIFFRACTION4B223 - 238
5X-RAY DIFFRACTION5B239 - 322
6X-RAY DIFFRACTION6B323 - 338
7X-RAY DIFFRACTION7C223 - 233
8X-RAY DIFFRACTION8C234 - 294
9X-RAY DIFFRACTION9C295 - 339

+
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