[English] 日本語
Yorodumi
- PDB-1t8b: Crystal structure of refolded PHOU-like protein (gi 2983430) from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t8b
TitleCrystal structure of refolded PHOU-like protein (gi 2983430) from Aquifex aeolicus
ComponentsPhosphate transport system protein phoU homolog
KeywordsTRANSPORT PROTEIN / alpha-helical protein consisting of two 3-helix bundles / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


negative regulation of phosphate transmembrane transport / negative regulation of phosphate metabolic process / phosphate ion transport / intracellular phosphate ion homeostasis / negative regulation of gene expression / protein homodimerization activity / cytoplasm
Similarity search - Function
Phosphate transport system protein PhoU / PhoU domain / PhoU domain / Phosphate transport system protein phou homolog 2; domain 2 / PhoU-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphate-specific transport system accessory protein PhoU homolog
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 3.23 Å
AuthorsOganesyan, V. / Kim, S.-H. / Oganesyan, N. / Jancarik, J. / Adams, P.D. / Kim, R. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Bacteriol. / Year: 2005
Title: Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus.
Authors: Oganesyan, V. / Oganesyan, N. / Adams, P.D. / Jancarik, J. / Yokota, H.A. / Kim, R. / Kim, S.H.
History
DepositionMay 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphate transport system protein phoU homolog
B: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)51,8902
Polymers51,8902
Non-polymers00
Water00
1
A: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)25,9451
Polymers25,9451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)25,9451
Polymers25,9451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Phosphate transport system protein phoU homolog

B: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)51,8902
Polymers51,8902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-y+1,x-y,z-1/31
Buried area3090 Å2
ΔGint-16 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.094, 85.094, 62.825
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 7 - 214 / Label seq-ID: 7 - 214

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsBiological assembly is monomeric

-
Components

#1: Protein Phosphate transport system protein phoU homolog


Mass: 25944.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: PHOU, AQ_906 / Plasmid: pB4.1105B / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: O67053

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Lithium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 10, 2004 / Details: double Si(111) crystal
RadiationMonochromator: double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.23→48 Å / Num. obs: 8109 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 120 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 14
Reflection shellResolution: 3.23→3.393 Å / Redundancy: 2 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.78 / % possible all: 90

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Blu-Icedata collection
SCALEPACKdata scaling
MOLREPphasing
SOLVEphasing
PHENIXphasing
RefinementMethod to determine structure: SAD, molecular replacement
Starting model: pdb entry 1T72

1t72


Resolution: 3.23→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 33.07 / SU ML: 0.532 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.541 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Matrix scaling, diagonal term 0.02
RfactorNum. reflection% reflectionSelection details
Rfree0.24846 367 4.6 %RANDOM
Rwork0.21427 ---
obs0.21596 7667 99.09 %-
all-8109 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 128.948 Å2
Baniso -1Baniso -2Baniso -3
1--3.79 Å2-1.89 Å20 Å2
2---3.79 Å20 Å2
3---5.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.532 Å0.541 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3.23→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 0 3358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223396
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9824572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8055414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022494
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.21869
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3740.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3181.52078
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70523366
X-RAY DIFFRACTIONr_scbond_it1.39531318
X-RAY DIFFRACTIONr_scangle_it2.6124.51206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1679 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.050.5
LS refinement shellResolution: 3.23→3.393 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.385 47
Rwork0.365 1037
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)
116.6352-6.22060.781914.3329-2.24423.8774-1.81520.86960.1078-0.25410.51310.06970.3561-0.31521.30210.374-0.2743-0.23660.2560.07660.32113.9785.8180.147
219.7933-5.5181.50029.44550.97474.3883-0.26660.51930.12031.5935-0.6847-0.19080.3347-0.07840.95130.5704-0.2153-0.15150.1420.13960.312140.62139.55929.471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 2147 - 214
2X-RAY DIFFRACTION2BB7 - 2147 - 214

+
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