[English] 日本語
Yorodumi
- PDB-2ffa: Crystal structure of ABC-ATPase H662A of the ABC-transporter HlyB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ffa
TitleCrystal structure of ABC-ATPase H662A of the ABC-transporter HlyB in complex with ADP
ComponentsAlpha-hemolysin translocation ATP-binding protein hlyB
KeywordsTRANSPORT PROTEIN / ABC-transporter / ATPase
Function / homology
Function and homology information


type I protein secretion system complex / protein secretion by the type I secretion system / ABC-type oligopeptide transporter activity / peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily ...ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Alpha-hemolysin translocation ATP-binding protein HlyB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZaitseva, J. / Oswald, C. / Jumpertz, T. / Jenewein, S. / Holland, I.B. / Schmitt, L.
CitationJournal: Embo J. / Year: 2006
Title: A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer.
Authors: Zaitseva, J. / Oswald, C. / Jumpertz, T. / Jenewein, S. / Wiedenmann, A. / Holland, I.B. / Schmitt, L.
History
DepositionDec 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 30, 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: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2313
Polymers27,6861
Non-polymers5452
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.156, 34.770, 38.100
Angle α, β, γ (deg.)90.00, 98.58, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Alpha-hemolysin translocation ATP-binding protein hlyB


Mass: 27685.781 Da / Num. of mol.: 1 / Fragment: amino acids 467-707 / Mutation: H662A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hlyB / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P08716
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris, 10% PEG 6000, 5% MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 24609 / % possible obs: 99.2 % / Observed criterion σ(F): 3.2 / Redundancy: 12.2 % / Rsym value: 0.062 / Net I/σ(I): 26
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.163 / % possible all: 88.5

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MT0

1mt0


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.619 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24033 1276 4.9 %RANDOM
Rwork0.20511 ---
obs0.20683 24609 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.059 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-1.87 Å2
2---0.61 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 35 243 2185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211971
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9812666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1475242
X-RAY DIFFRACTIONr_chiral_restr0.1130.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021445
X-RAY DIFFRACTIONr_nbd_refined0.2160.2972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.215
X-RAY DIFFRACTIONr_mcbond_it1.1171.51202
X-RAY DIFFRACTIONr_mcangle_it2.0821941
X-RAY DIFFRACTIONr_scbond_it2.9453769
X-RAY DIFFRACTIONr_scangle_it4.8134.5725
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 89
Rwork0.243 1840
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)
10.5833-0.5863-0.06541.1905-0.22290.6256-0.0206-0.06090.0394-0.0020.08510.02380.0299-0.0643-0.06450.1197-0.00730.02390.14420.00660.0993237.847520.8716-19.1583
25.03580.89462.22560.36590.19212.4105-0.38440.23910.50150.2068-0.0355-0.1799-0.23230.10870.41990.1025-0.0037-0.1510.09210.03310.2723261.663828.5793-7.5458
30.3553-0.12820.19591.19340.59370.97620.0076-0.01670.0147-0.08470.046-0.20530.110.0978-0.05360.13210.01250.04190.14130.0120.1225252.473410.352-22.7855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA465 - 5505 - 90
2X-RAY DIFFRACTION2AA551 - 62591 - 165
3X-RAY DIFFRACTION3AA626 - 707166 - 247

+
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