[English] 日本語
Yorodumi
- PDB-3nje: Structure of the Minor Pseudopilin XcpW from the Pseudomonas aeru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nje
TitleStructure of the Minor Pseudopilin XcpW from the Pseudomonas aeruginosa Type II Secretion System
ComponentsGeneral secretion pathway protein J
KeywordsPROTEIN TRANSPORT / Type II secretion / Pseudopilin / minor pilin / pilin fold / secretion / XcpU / XcpV / XcpX
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane
Similarity search - Function
Type II secretion system protein GspJ / Type II secretion system (T2SS), protein J / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Type II secretion system protein J
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFranz, L.P. / Dyer, D.H. / Voulhoux, R. / Forest, K.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of the minor pseudopilin XcpW from the Pseudomonas aeruginosa type II secretion system.
Authors: Franz, L.P. / Douzi, B. / Durand, E. / Dyer, D.H. / Voulhoux, R. / Forest, K.T.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: General secretion pathway protein J
B: General secretion pathway protein J


Theoretical massNumber of molelcules
Total (without water)48,4042
Polymers48,4042
Non-polymers00
Water3,477193
1
A: General secretion pathway protein J


Theoretical massNumber of molelcules
Total (without water)24,2021
Polymers24,2021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: General secretion pathway protein J


Theoretical massNumber of molelcules
Total (without water)24,2021
Polymers24,2021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.718, 82.911, 57.777
Angle α, β, γ (deg.)90.00, 105.41, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein General secretion pathway protein J / PilD-dependent protein pddD / xcpW


Mass: 24201.885 Da / Num. of mol.: 2 / Fragment: UNP residues 28-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: xcpW, pddD / Plasmid: pETG-20A-WJ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q00517
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1.89 Å3/Da / Density % sol: 35.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 15mM KCl, 7.5% PEG 8000, 0.1M ATP, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 30798 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.043 / Net I/σ(I): 35.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 1550 / Rsym value: 0.351 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CI0

3ci0


Resolution: 1.85→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.111 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 1545 5 %RANDOM
Rwork0.1944 ---
obs0.19631 29187 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.937 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å2-0.07 Å2
2--1.79 Å20 Å2
3----0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.136 Å0.147 Å
Refinement stepCycle: LAST / Resolution: 1.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 0 193 2861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212729
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9463688
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3015319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57422.658158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55615492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6481542
X-RAY DIFFRACTIONr_chiral_restr0.0890.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212132
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7281.51590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36722552
X-RAY DIFFRACTIONr_scbond_it1.92631139
X-RAY DIFFRACTIONr_scangle_it3.214.51135
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 89 -
Rwork0.224 2161 -
obs--98.38 %
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)
113.5784-9.5622-4.967610.9782.69633.0545-0.0691-0.1906-0.66750.1119-0.12080.26890.39920.0430.18990.2161-0.0091-0.02770.02920.02360.095634.05841.602826.5814
28.6766-3.13250.05353.61890.47192.8816-0.01960.1564-0.36430.1133-0.18470.35620.1752-0.23190.20440.0372-0.02860.02990.033-0.0280.06816.293414.815929.4628
30.2152-0.6661-0.78382.19272.35613.33080.0141-0.00990.04810.1152-0.0438-0.0904-0.17090.13180.02980.1969-0.0372-0.00920.1317-0.0540.180418.768829.908237.9579
48.45480.4929-2.49514.0872-0.55826.5016-0.2021-0.4885-0.0650.0149-0.0203-0.08290.01260.30920.22250.01380.016-0.0020.0523-0.01290.037622.62120.997932.6604
52.6696-0.5198-0.01031.81990.45912.312-0.0916-0.24930.16250.09680.07940.0506-0.13640.00360.01220.02180.00230.00660.0477-0.01880.05324.645320.967531.6684
63.8998-0.8409-0.22951.18280.47751.95720.01740.24140.0769-0.0281-0.04040.0695-0.0762-0.13770.0230.0101-0.0006-0.0010.0378-0.01030.042520.153420.120323.3226
716.3802-3.3338-12.740519.35446.117820.7927-0.36731.2752-1.2013-0.9734-0.3875-1.50811.09331.18210.75480.33380.12340.07220.6036-0.01660.362534.426337.74737.2192
82.8196-0.0657-0.39271.93310.52943.2021-0.0074-0.1896-0.15510.2026-0.00320.03730.2308-0.21260.01070.0617-0.0476-0.01020.0690.02350.029317.135242.843956.3234
91.2879-0.8633-0.26251.10920.75671.62360.0367-0.2104-0.31440.1547-0.07660.05130.3316-0.06940.03990.1636-0.0714-0.01720.16820.10130.190620.644937.917456.0567
104.35070.9831-1.11761.5072-0.22111.8537-0.07830.035-0.3139-0.06680.0717-0.25480.31240.18610.00660.06730.0138-0.01730.10040.02170.084833.663443.030348.8311
112.68690.7697-1.18991.4435-1.20245.68260.1209-0.06070.41660.17610.01450.1377-0.5289-0.4754-0.13540.05580.03130.02020.0823-0.02960.072516.572156.938858.0831
127.48680.0035-1.97650.5265-0.30841.86420.00690.26340.0556-0.1144-0.020.00240.118-0.07060.01310.0281-0.00290.0010.08030.01660.019223.123249.990145.8013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 53
2X-RAY DIFFRACTION2A54 - 67
3X-RAY DIFFRACTION3A68 - 83
4X-RAY DIFFRACTION4A84 - 109
5X-RAY DIFFRACTION5A110 - 166
6X-RAY DIFFRACTION6A167 - 206
7X-RAY DIFFRACTION7B43 - 50
8X-RAY DIFFRACTION8B51 - 80
9X-RAY DIFFRACTION9B81 - 138
10X-RAY DIFFRACTION10B139 - 149
11X-RAY DIFFRACTION11B150 - 179
12X-RAY DIFFRACTION12B180 - 206

+
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