[English] 日本語
Yorodumi
- PDB-2hpg: The crystal structure of a thermophilic TRAP periplasmic binding ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hpg
TitleThe crystal structure of a thermophilic TRAP periplasmic binding protein
ComponentsABC transporter, periplasmic substrate-binding protein
KeywordsLIGAND BINDING PROTEIN / periplasmic binding protein / thermophilic proteins / TRAP-transport
Function / homology
Function and homology information


transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter, periplasmic substrate-binding protein, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsCuneo, M.J. / Hellinga, H.W.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural analysis of a periplasmic binding protein in the tripartite ATP-independent transporter family reveals a tetrameric assembly that may have a role in ligand transport.
Authors: Cuneo, M.J. / Changela, A. / Miklos, A.E. / Beese, L.S. / Krueger, J.K. / Hellinga, H.W.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC transporter, periplasmic substrate-binding protein
B: ABC transporter, periplasmic substrate-binding protein
C: ABC transporter, periplasmic substrate-binding protein
D: ABC transporter, periplasmic substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)151,3514
Polymers151,3514
Non-polymers00
Water9,530529
1
A: ABC transporter, periplasmic substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)37,8381
Polymers37,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, periplasmic substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)37,8381
Polymers37,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ABC transporter, periplasmic substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)37,8381
Polymers37,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ABC transporter, periplasmic substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)37,8381
Polymers37,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.260, 119.260, 429.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a monomer.

-
Components

#1: Protein
ABC transporter, periplasmic substrate-binding protein / TRAP-Periplasmic Binding Protein


Mass: 37837.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm0322 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta / References: UniProt: Q9WYF8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M Phosphate/Citrate pH4.2, 2.5M Ammonium Sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97167, 0.97934, 0.97920
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971671
20.979341
30.97921
ReflectionResolution: 1.9→103.282 Å / Num. all: 142555 / Num. obs: 142555 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-28.40.4051.9171983204710.405100
2-2.128.90.3352.2173500194110.335100
2.12-2.279.40.2612.9172072182540.261100
2.27-2.459.80.2093.6167230170670.209100
2.45-2.6910.10.1584.7158510157680.158100
2.69-310.30.1126.5147350143540.112100
3-3.4710.20.0877.6129776127200.087100
3.47-4.2510.20.0659.8110703109020.065100
4.25-6.0110.10.05112.18706585940.051100
6.01-30.019.50.03913.94765350140.03999.2

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.906 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 7152 5 %RANDOM
Rwork0.213 ---
all0.215 142411 --
obs0.215 142411 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.493 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å20 Å2
2--1.1 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10353 0 0 529 10882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210615
X-RAY DIFFRACTIONr_bond_other_d0.0010.027372
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.96314375
X-RAY DIFFRACTIONr_angle_other_deg0.872318086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84451335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39825.071493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.701151985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5951545
X-RAY DIFFRACTIONr_chiral_restr0.0730.21540
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022092
X-RAY DIFFRACTIONr_nbd_refined0.210.22276
X-RAY DIFFRACTIONr_nbd_other0.1830.27653
X-RAY DIFFRACTIONr_nbtor_refined0.180.25128
X-RAY DIFFRACTIONr_nbtor_other0.0850.25333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2511
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.217
X-RAY DIFFRACTIONr_mcbond_it0.8751.58058
X-RAY DIFFRACTIONr_mcbond_other0.131.52614
X-RAY DIFFRACTIONr_mcangle_it1.017210365
X-RAY DIFFRACTIONr_scbond_it1.75134895
X-RAY DIFFRACTIONr_scangle_it2.5614.53980
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 486 -
Rwork0.314 9847 -
obs-10333 100 %

+
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