[English] 日本語
Yorodumi
- PDB-4u02: Crystal structure of apo-TTHA1159 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u02
TitleCrystal structure of apo-TTHA1159
ComponentsAmino acid ABC transporter, ATP-binding protein
KeywordsTRANSPORT PROTEIN / ATP binding protein / ABC amino acid transporter / Nucleotide binding domain
Function / homology
Function and homology information


ABC-type amino acid transporter activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
ABC-type amino acid transport system, ATPase component, HisP-type / : / 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 ...ABC-type amino acid transport system, ATPase component, HisP-type / : / 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
Amino acid ABC transporter, ATP-binding protein
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsKarthiga Devi, S. / Chichili, V.P.R. / Velmurugan, D. / Sivaraman, J.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural basis for the hydrolysis of ATP by a nucleotide binding subunit of an amino acid ABC transporter from Thermus thermophilus
Authors: Devi, S.K. / Chichili, V.P. / Jeyakanthan, J. / Velmurugan, D. / Sivaraman, J.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amino acid ABC transporter, ATP-binding protein
B: Amino acid ABC transporter, ATP-binding protein
C: Amino acid ABC transporter, ATP-binding protein
D: Amino acid ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7068
Polymers111,3224
Non-polymers3844
Water5,477304
1
A: Amino acid ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9262
Polymers27,8301
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area11630 Å2
MethodPISA
2
B: Amino acid ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9262
Polymers27,8301
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area11720 Å2
MethodPISA
3
C: Amino acid ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9262
Polymers27,8301
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area11650 Å2
MethodPISA
4
D: Amino acid ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9262
Polymers27,8301
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.669, 130.131, 74.972
Angle α, β, γ (deg.)90.00, 93.82, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Amino acid ABC transporter, ATP-binding protein


Mass: 27830.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA1159 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJ55
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES, 0.2M Ammonium chloride, 20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 38334 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rsym value: 0.06 / Net I/σ(I): 29.2

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.399→31.225 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1949 5.17 %
Rwork0.2009 --
obs0.2035 37677 93.75 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.683 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.3905 Å2-0 Å2-0.0919 Å2
2---1.0367 Å2-0 Å2
3----6.3537 Å2
Refinement stepCycle: LAST / Resolution: 2.399→31.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7698 0 20 304 8022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037842
X-RAY DIFFRACTIONf_angle_d0.76210567
X-RAY DIFFRACTIONf_dihedral_angle_d14.8463063
X-RAY DIFFRACTIONf_chiral_restr0.0521183
X-RAY DIFFRACTIONf_plane_restr0.0031386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3987-2.45870.27121200.20722347X-RAY DIFFRACTION86
2.4587-2.52510.34211390.21842370X-RAY DIFFRACTION88
2.5251-2.59940.30031270.24482389X-RAY DIFFRACTION88
2.5994-2.68330.27731410.22072424X-RAY DIFFRACTION89
2.6833-2.77910.29031360.23112367X-RAY DIFFRACTION88
2.7791-2.89030.29141350.22592508X-RAY DIFFRACTION92
2.8903-3.02170.27451350.22532530X-RAY DIFFRACTION93
3.0217-3.18090.2991470.21592615X-RAY DIFFRACTION96
3.1809-3.380.2711360.2062661X-RAY DIFFRACTION98
3.38-3.64060.22561450.18882671X-RAY DIFFRACTION99
3.6406-4.00630.20641530.17322689X-RAY DIFFRACTION99
4.0063-4.58440.2241370.15612696X-RAY DIFFRACTION99
4.5844-5.76990.19681500.19162718X-RAY DIFFRACTION99
5.7699-31.22720.24531480.2282743X-RAY DIFFRACTION99

+
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