[English] 日本語
Yorodumi
- PDB-3vzu: Crystal Structure of outer membrane protein PorB from Neisseria m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vzu
TitleCrystal Structure of outer membrane protein PorB from Neisseria meningitidis in complex with AMP-PNP
Componentsouter membrane protein
KeywordsMEMBRANE PROTEIN / Beta-barrel / porin / channel / outer membrane protein / transport
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Major outer membrane protein P.IB
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTanabe, M. / Iverson, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB.
Authors: Tanabe, M. / Nimigean, C.M. / Iverson, T.M.
History
DepositionOct 15, 2012Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 13, 2013ID: 3A2U
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
X: outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6862
Polymers38,1791
Non-polymers5061
Water00
1
X: outer membrane protein
hetero molecules

X: outer membrane protein
hetero molecules

X: outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0576
Polymers114,5383
Non-polymers1,5193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10640 Å2
ΔGint-55 kcal/mol
Surface area44680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.482, 84.482, 106.302
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein outer membrane protein


Mass: 38179.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: W135 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: M4GGR4*PLUS
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM MES, 50mM CsCl, 28-32% Jeffamine M-600, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 31, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→42.26 Å / Num. all: 9609 / Num. obs: 8668 / % possible obs: 91.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.338 / % possible all: 47

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A2R

3a2r
PDB Unreleased entry


Resolution: 2.9→39.26 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27331 438 5.1 %RANDOM
Rwork0.23741 ---
obs0.23933 8229 90.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.663 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å2-0 Å2
2--0.5 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 31 0 2624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022675
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0641.9383614
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.8715340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05224.444126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.66315431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6061514
X-RAY DIFFRACTIONr_chiral_restr0.1340.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022058
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 14 -
Rwork0.391 310 -
obs--46.69 %

+
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