[English] 日本語
Yorodumi
- PDB-4aui: STRUCTURE AND FUNCTION OF THE PORB PORIN FROM DISSEMINATING N. GO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aui
TitleSTRUCTURE AND FUNCTION OF THE PORB PORIN FROM DISSEMINATING N. GONORRHOEAE
Components
  • POLY ALA
  • PORIN (PORB)
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE PROTEIN / INFECTION / INVASION
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / ATP binding
Similarity search - Function
Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Porin (PorB)
Similarity search - Component
Biological speciesNEISSERIA GONORRHOEAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZeth, K. / Kozjak-Pavlovic, V. / Faulstich, M. / Hurwitz, R. / Kepp, O. / Rudel, T.
CitationJournal: Biochem.J. / Year: 2013
Title: Structure and Function of the Porb Porin from Disseminating Neisseria Gonorrhoeae.
Authors: Zeth, K. / Kozjak-Pavlovic, V. / Faulstich, M. / Fraunholz, M. / Hurwitz, R. / Kepp, O. / Rudel, T.
History
DepositionMay 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Oct 9, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Source and taxonomy / Structure summary
Category: entity / entity_src_nat ...entity / entity_src_nat / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _entity.src_method / _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PORIN (PORB)
B: PORIN (PORB)
C: PORIN (PORB)
D: POLY ALA
E: POLY ALA
F: POLY ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,41816
Polymers109,3036
Non-polymers2,11610
Water0
1
A: PORIN (PORB)
B: PORIN (PORB)
C: PORIN (PORB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,65913
Polymers107,5433
Non-polymers2,11610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-101.6 kcal/mol
Surface area41780 Å2
MethodPISA
2
D: POLY ALA


  • defined by software
  • 587 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5871
Polymers5871
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: POLY ALA


  • defined by software
  • 587 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5871
Polymers5871
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
F: POLY ALA


  • defined by software
  • 587 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5871
Polymers5871
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.050, 111.470, 88.340
Angle α, β, γ (deg.)90.00, 102.07, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:21 OR RESSEQ 26:182 OR RESSEQ 185:214 OR RESSEQ 219:250 OR RESSEQ 257:308 )
211CHAIN B AND (RESSEQ 1:21 OR RESSEQ 26:182 OR RESSEQ 185:214 OR RESSEQ 219:250 OR RESSEQ 257:308 )
311CHAIN C AND (RESSEQ 1:21 OR RESSEQ 26:182 OR RESSEQ 185:214 OR RESSEQ 219:250 OR RESSEQ 257:308 )

-
Components

#1: Protein PORIN (PORB)


Mass: 35847.633 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) NEISSERIA GONORRHOEAE (bacteria) / References: UniProt: Q51056
#2: Protein/peptide POLY ALA


Mass: 586.638 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) NEISSERIA GONORRHOEAE (bacteria)
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.03 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→38 Å / Num. obs: 14044 / % possible obs: 98 % / Observed criterion σ(I): 1.7 / Redundancy: 3.9 % / Biso Wilson estimate: 80.38 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 5.9
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.7 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A2R

3a2r
PDB Unreleased entry


Resolution: 3.2→38.05 Å / SU ML: 0.58 / σ(F): 1.35 / Phase error: 31.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 700 5 %
Rwork0.2212 --
obs0.2236 14044 78.39 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 109.437 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6253 Å2-0 Å2-4.3982 Å2
2---0.0794 Å20 Å2
3----0.546 Å2
Refinement stepCycle: LAST / Resolution: 3.2→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7205 0 124 0 7329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0227906
X-RAY DIFFRACTIONf_angle_d1.93810154
X-RAY DIFFRACTIONf_dihedral_angle_d20.6442590
X-RAY DIFFRACTIONf_chiral_restr0.1211052
X-RAY DIFFRACTIONf_plane_restr0.0071327
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2266X-RAY DIFFRACTIONPOSITIONAL
12B2266X-RAY DIFFRACTIONPOSITIONAL0.147
13C2266X-RAY DIFFRACTIONPOSITIONAL0.169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-3.44720.42671400.32832703X-RAY DIFFRACTION80
3.4472-3.79380.30181430.25432687X-RAY DIFFRACTION79
3.7938-4.34210.26281380.19292626X-RAY DIFFRACTION78
4.3421-5.4680.24221400.17572663X-RAY DIFFRACTION78
5.468-38.0530.22861390.22892665X-RAY DIFFRACTION77
Refinement TLS params.Method: refined / Origin x: 30.5299 Å / Origin y: -0.3243 Å / Origin z: 29.5565 Å
111213212223313233
T0.2047 Å20.0382 Å2-0.049 Å2-0.2566 Å20.0009 Å2--0.212 Å2
L0.5543 °20.3578 °2-0.0359 °2-1.0885 °2-0.3449 °2--0.5215 °2
S0.075 Å °-0.1292 Å °0.0535 Å °0.279 Å °-0.0997 Å °-0.0645 Å °-0.1121 Å °0.1104 Å °-0.0109 Å °
Refinement TLS groupSelection details: ALL

+
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