[English] 日本語
Yorodumi
- PDB-3b5y: Crystal Structure of MsbA from Salmonella typhimurium with AMPPNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b5y
TitleCrystal Structure of MsbA from Salmonella typhimurium with AMPPNP
ComponentsLipid A export ATP-binding/permease protein msbA
KeywordsMEMBRANE PROTEIN / ABC transporter / MsbA / lipid flippase / ATP-binding / Hydrolase / Inner membrane / Lipid transport / Membrane / Nucleotide-binding / Transmembrane
Function / homology
Function and homology information


ABC-type lipid A-core oligosaccharide transporter / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter, lipid A-core flippase, MsbA / 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 ...Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter, lipid A-core flippase, MsbA / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATP-dependent lipid A-core flippase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.5 Å
AuthorsWard, A. / Reyes, C.L. / Yu, J. / Roth, C.B. / Chang, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Flexibility in the ABC transporter MsbA: Alternating access with a twist.
Authors: Ward, A. / Reyes, C.L. / Yu, J. / Roth, C.B. / Chang, G.
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
A: Lipid A export ATP-binding/permease protein msbA
B: Lipid A export ATP-binding/permease protein msbA
C: Lipid A export ATP-binding/permease protein msbA
D: Lipid A export ATP-binding/permease protein msbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,6598
Polymers257,6344
Non-polymers2,0254
Water0
1
A: Lipid A export ATP-binding/permease protein msbA
B: Lipid A export ATP-binding/permease protein msbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8294
Polymers128,8172
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lipid A export ATP-binding/permease protein msbA
D: Lipid A export ATP-binding/permease protein msbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8294
Polymers128,8172
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)262.929, 121.236, 173.119
Angle α, β, γ (deg.)90.00, 121.89, 90.00
Int Tables number5
Space group name H-MC121
Detailsbiological unit is a dimer. there are 2 biological units in the asymmetric unit (chains A & B and chains C & D)

-
Components

#1: Protein
Lipid A export ATP-binding/permease protein msbA / Coordinate model: Cα atoms only


Mass: 64408.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: msbA / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P63359, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.55 Å3/Da / Density % sol: 72.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM NaCl, 18-24% PEG 350MME, 10 mM AMPPNP, 2.5mM MgCl2 and 0.05% beta-UDM, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211.0063, 1.0089
SYNCHROTRONALS 8.3.121.0063, 1.0089
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00631
21.00891
ReflectionResolution: 4.5→20 Å / Num. all: 25959 / Num. obs: 25959 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.089
Reflection shellResolution: 4.5→4.78 Å / Num. unique all: 3571 / % possible all: 87.7

-
Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementResolution: 4.5→19.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 63239.398 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: This entry contains C-alpha atoms only; BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.343 2606 10 %RANDOM
Rwork0.295 ---
obs-25959 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 126.936 Å2 / ksol: 0.2 e/Å3
Displacement parametersBiso mean: 220.2 Å2
Baniso -1Baniso -2Baniso -3
1-60.2 Å20 Å222.54 Å2
2---50.81 Å20 Å2
3----9.39 Å2
Refinement stepCycle: LAST / Resolution: 4.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 124 0 2412
LS refinement shellResolution: 4.5→4.78 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.491 390 9.8 %
Rwork0.472 3571 -
all-3961 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2atp.par

+
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