[English] 日本語
Yorodumi
- PDB-2fgk: Crystal structure of the ABC-cassette E631Q mutant of HlyB with b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fgk
TitleCrystal structure of the ABC-cassette E631Q mutant of HlyB with bound ATP
ComponentsAlpha-hemolysin translocation ATP-binding protein hlyB
KeywordsTRANSPORT PROTEIN / ABC-transporter / ABC-cassette / ATP-loaded dimer
Function / homology
Function and homology information


type I protein secretion system complex / protein secretion by the type I secretion system / ATPase-coupled lipid transmembrane transporter activity / ABC-type 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 C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / 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 C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / 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'-TRIPHOSPHATE / Alpha-hemolysin translocation ATP-binding protein HlyB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 22, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-hemolysin translocation ATP-binding protein hlyB
B: Alpha-hemolysin translocation ATP-binding protein hlyB
C: Alpha-hemolysin translocation ATP-binding protein hlyB
D: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0368
Polymers111,0074
Non-polymers2,0294
Water2,738152
1
A: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2592
Polymers27,7521
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2592
Polymers27,7521
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2592
Polymers27,7521
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2592
Polymers27,7521
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.142, 189.256, 63.475
Angle α, β, γ (deg.)90.00, 111.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31A
41C
12B
22D
32B
42D

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPLEULEUAA467 - 5497 - 89
211ASPASPLEULEUCC467 - 5497 - 89
321LYSLYSASPASPAA625 - 707165 - 247
421LYSLYSASPASPCC625 - 707165 - 247
112ASPASPLEULEUBB467 - 5497 - 89
212ASPASPLEULEUDD467 - 5497 - 89
322LYSLYSASPASPBB625 - 707165 - 247
422LYSLYSASPASPDD625 - 707165 - 247

NCS ensembles :
ID
1
2

-
Components

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


Mass: 27751.865 Da / Num. of mol.: 4 / Fragment: amino acids 467-707 / Mutation: E631Q
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): DH5 alpha / References: UniProt: P08716
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris, PEG 6000, MPD, pH 8.5, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 26969 / Num. obs: 26565 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rsym value: 0.094
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 5.2 / Rsym value: 0.257 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1XEF

1xef


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.897 / SU B: 29.83 / SU ML: 0.33 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 5.2 / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28022 1406 5 %RANDOM
Rwork0.22302 ---
obs0.22599 26565 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.569 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å2-3.78 Å2
2--1.53 Å20 Å2
3----5.84 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7572 0 124 152 7848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227812
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.99110572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16124.091352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.046151436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9261564
X-RAY DIFFRACTIONr_chiral_restr0.0770.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025744
X-RAY DIFFRACTIONr_nbd_refined0.1960.23710
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.210
X-RAY DIFFRACTIONr_mcbond_it0.361.54935
X-RAY DIFFRACTIONr_mcangle_it0.63927712
X-RAY DIFFRACTIONr_scbond_it0.77633237
X-RAY DIFFRACTIONr_scangle_it1.2484.52860
Refine LS restraints NCS

Dom-ID: 1 / Number: 1332 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.010.05
2Btight positional0.010.05
1Atight thermal0.030.5
2Btight thermal0.030.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 110 -
Rwork0.293 1999 -
obs--99.25 %
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)
12.55160.2863-0.4424.8184-0.08695.0779-0.17420.1181-0.3677-0.79810.1071-0.0230.4119-0.09990.0672-0.0989-0.01780.0806-0.159-0.0638-0.15270.6574-3.1892-9.4281
26.2021-0.4685-3.82425.58017.980319.0433-1.21130.4945-0.77522.0452-0.74521.15554.0671-1.26771.95650.9708-0.14980.5788-0.2029-0.06230.1862-4.1534-18.21519.0944
31.4896-0.4733-1.63753.22760.64179.0943-0.059-0.41530.09520.62030.202-0.25470.4750.7631-0.143-0.1870.0574-0.0389-0.0344-0.0284-0.1524-0.30155.116922.3612
45.4541-2.13171.85396.02951.51124.90180.0458-0.2652-0.46190.38860.020.67710.1752-0.7934-0.0658-0.31720.01410.068-0.09370.1063-0.0579-15.067613.55294.9937
52.56160.13770.61125.0141-0.35625.1607-0.17760.14010.358-0.79750.10890.0919-0.40120.11830.0687-0.1319-0.0206-0.0738-0.17310.0409-0.1575-24.202-47.5208-9.434
67.5439-0.60325.00767.005-8.371121.5728-1.30540.11680.93442.1006-0.7632-1.5685-4.4271.39722.06860.9501-0.1899-0.5858-0.17440.060.3749-19.4022-32.53988.9955
71.2658-0.30821.42342.6146-0.21339.17010.002-0.4061-0.11950.56620.17440.2181-0.4063-0.7914-0.1765-0.15280.06110.0478-0.0320.0377-0.1306-23.3169-55.843522.3666
83.3527-1.506-0.82516.4492-1.20084.5883-0.0772-0.29280.38240.4302-0.0207-0.7199-0.10930.8680.0979-0.32810.011-0.0406-0.0544-0.0804-0.0458-8.4845-64.26995.0585
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA467 - 5497 - 89
2X-RAY DIFFRACTION1AA626 - 707166 - 247
3X-RAY DIFFRACTION2AA550 - 62590 - 165
4X-RAY DIFFRACTION3BB467 - 5497 - 89
5X-RAY DIFFRACTION3BB626 - 707166 - 247
6X-RAY DIFFRACTION4BB550 - 62590 - 165
7X-RAY DIFFRACTION5CC467 - 5497 - 89
8X-RAY DIFFRACTION5CC626 - 707166 - 247
9X-RAY DIFFRACTION6CC550 - 62590 - 165
10X-RAY DIFFRACTION7DD467 - 5497 - 89
11X-RAY DIFFRACTION7DD626 - 707166 - 247
12X-RAY DIFFRACTION8DD550 - 62590 - 165

+
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