[English] 日本語
Yorodumi
- PDB-3fh6: Crystal structure of the resting state maltose transporter from E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fh6
TitleCrystal structure of the resting state maltose transporter from E. coli
Components
  • Maltose transport system permease protein malF
  • Maltose transport system permease protein malG
  • Maltose/maltodextrin import ATP-binding protein malK
KeywordsTRANSPORT PROTEIN / maltose transporter / ground state / ABC transporter / membrane protein / Cell inner membrane / Cell membrane / Membrane / Sugar transport / Transmembrane / Transport / ATP-binding / Hydrolase / Nucleotide-binding
Function / homology
Function and homology information


ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / maltose transport complex / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / maltose transport complex / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / DNA-binding transcription factor binding / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain / MalF, N-terminal region, transmembrane helices / Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / : ...Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain / MalF, N-terminal region, transmembrane helices / Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / : / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / 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. / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Maltose/maltodextrin transport system permease protein MalF / Maltose/maltodextrin transport system permease protein MalG / Maltose/maltodextrin import ATP-binding protein MalK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4.5 Å
AuthorsKhare, D. / Oldham, M.L. / Orelle, C. / Davidson, A.L. / Chen, J.
CitationJournal: Mol.Cell / Year: 2009
Title: Alternating access in maltose transporter mediated by rigid-body rotations.
Authors: Khare, D. / Oldham, M.L. / Orelle, C. / Davidson, A.L. / Chen, J.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Maltose transport system permease protein malF
G: Maltose transport system permease protein malG
A: Maltose/maltodextrin import ATP-binding protein malK
B: Maltose/maltodextrin import ATP-binding protein malK
H: Maltose transport system permease protein malF
I: Maltose transport system permease protein malG
C: Maltose/maltodextrin import ATP-binding protein malK
D: Maltose/maltodextrin import ATP-binding protein malK


Theoretical massNumber of molelcules
Total (without water)339,4178
Polymers339,4178
Non-polymers00
Water00
1
F: Maltose transport system permease protein malF
G: Maltose transport system permease protein malG
A: Maltose/maltodextrin import ATP-binding protein malK
B: Maltose/maltodextrin import ATP-binding protein malK


Theoretical massNumber of molelcules
Total (without water)169,7084
Polymers169,7084
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-112 kcal/mol
Surface area62150 Å2
MethodPISA
2
H: Maltose transport system permease protein malF
I: Maltose transport system permease protein malG
C: Maltose/maltodextrin import ATP-binding protein malK
D: Maltose/maltodextrin import ATP-binding protein malK


Theoretical massNumber of molelcules
Total (without water)169,7084
Polymers169,7084
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-112 kcal/mol
Surface area62150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.097, 209.480, 438.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.88774, 0.08265, 0.45286), (-0.09761, 0.99518, 0.00972), (-0.44987, -0.05283, 0.89153)
Vector: 24.0031, -64.79521, -0.99527)

-
Components

#1: Protein Maltose transport system permease protein malF


Mass: 53093.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4033, JW3993, malF / Production host: Escherichia coli (E. coli) / References: UniProt: P02916
#2: Protein Maltose transport system permease protein malG


Mass: 32246.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4032, JW3992, malG / Production host: Escherichia coli (E. coli) / References: UniProt: P68183
#3: Protein
Maltose/maltodextrin import ATP-binding protein malK


Mass: 42184.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4035, JW3995, malK / Production host: Escherichia coli (E. coli) / References: UniProt: P68187, EC: 3.6.3.19

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.79 Å3/Da / Density % sol: 78.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 11.5 % PEG 4000, 0.1M ADA pH 6.5, 0.1 M NaCl, 0.1 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942, 0.9794, 0.9795, 0.9494
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2007
RadiationMonochromator: Si(111) double crystal / Protocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.97941
30.97951
40.94941
ReflectionResolution: 4.5→100 Å / Num. obs: 40160 / % possible obs: 87.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.126 / Χ2: 1.975 / Net I/σ(I): 11.126
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
4.5-4.662.50.78430222.038169.1
4.66-4.852.70.81531581.959172.2
4.85-5.072.80.68132952.001175.1
5.07-5.342.90.59934021.991177.8
5.34-5.673.10.61139252189.5
5.67-6.113.60.57143111.849197.7
6.11-6.723.90.37244101.956199.7
6.72-7.6940.21444252.245199.5
7.69-9.693.90.1144461.914199.3
9.69-1003.80.08643671.83193.9

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD
Starting model: PDB entries 1Q1B, 1Q1E, 2R6G

1q1b

1q1e

2r6g


Resolution: 4.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
Details: The structure was refined with strict NCS restraints applied to the refined molecules F,G,A,B. The molecules H,I,C,D that build the complete asymmetric unit, are the respective NCS-mates
RfactorNum. reflection% reflection
Rfree0.363 2012 4.3 %
Rwork0.34 --
obs-38761 85.2 %
Solvent computationBsol: 137.42 Å2
Displacement parametersBiso max: 521.43 Å2 / Biso mean: 300.466 Å2 / Biso min: 94.21 Å2
Refinement stepCycle: LAST / Resolution: 4.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20236 0 0 0 20236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.998
Xplor fileSerial no: 1 / Param file: protein_between.param

+
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