[English] 日本語
Yorodumi
- PDB-7d53: SpuA mutant - H221N with Glu -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d53
TitleSpuA mutant - H221N with Glu
ComponentsProbable glutamine amidotransferase
KeywordsHYDROLASE / SpuA / gama-glutamyl-gama-aminobutyrate hydrolase / glutamine amidotransferase / Pseudomonas aeruginosa PAO1.
Function / homology
Function and homology information


gamma-glutamyl-gamma-aminobutyrate hydrolase / gamma-glutamyl-gamma-aminobutyrate hydrolase activity / polyamine catabolic process / spermidine catabolic process / metal ion binding
Similarity search - Function
Peptidase C26, gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD-like / Peptidase C26 / Peptidase C26 / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / gamma-glutamyl-gamma-aminobutyrate hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, Y. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
National Natural Science Foundation of China (NSFC)31800627 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structure and mechanism of the gamma-glutamyl-gamma-aminobutyrate hydrolase SpuA from Pseudomonas aeruginosa.
Authors: Chen, Y. / Jia, H. / Zhang, J. / Liang, Y. / Liu, R. / Zhang, Q. / Bartlam, M.
History
DepositionSep 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable glutamine amidotransferase
B: Probable glutamine amidotransferase
C: Probable glutamine amidotransferase
D: Probable glutamine amidotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,61412
Polymers105,9284
Non-polymers6868
Water18,1231006
1
A: Probable glutamine amidotransferase
B: Probable glutamine amidotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3076
Polymers52,9642
Non-polymers3434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-35 kcal/mol
Surface area18780 Å2
MethodPISA
2
C: Probable glutamine amidotransferase
hetero molecules

D: Probable glutamine amidotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3076
Polymers52,9642
Non-polymers3434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area3270 Å2
ΔGint-35 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.349, 120.378, 158.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
Probable glutamine amidotransferase


Mass: 26482.100 Da / Num. of mol.: 4 / Mutation: H221N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: spuA, PA0297 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I6J4
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris-HCl pH 8.5, 30% w/v Polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 120939 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.93 Å2 / Rpim(I) all: 0.04 / Net I/σ(I): 27.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5983 / Rpim(I) all: 0.359 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D4R

7d4r


Resolution: 1.6→30.61 Å / SU ML: 0.1507 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.202 2000 1.66 %
Rwork0.1628 118801 -
obs0.1634 120801 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.86 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7430 0 4 1006 8440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01057606
X-RAY DIFFRACTIONf_angle_d1.06510360
X-RAY DIFFRACTIONf_chiral_restr0.06321148
X-RAY DIFFRACTIONf_plane_restr0.00811394
X-RAY DIFFRACTIONf_dihedral_angle_d13.62251058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.22781330.22237864X-RAY DIFFRACTION92.69
1.64-1.680.25161400.20998396X-RAY DIFFRACTION99.99
1.68-1.730.24811420.20438407X-RAY DIFFRACTION99.96
1.73-1.790.23321420.19588441X-RAY DIFFRACTION99.98
1.79-1.850.22781430.18658459X-RAY DIFFRACTION100
1.85-1.920.22771410.18618445X-RAY DIFFRACTION99.99
1.92-2.010.23111440.1758484X-RAY DIFFRACTION99.99
2.01-2.120.18151430.16468481X-RAY DIFFRACTION100
2.12-2.250.19631430.15448547X-RAY DIFFRACTION100
2.25-2.420.18051420.15688472X-RAY DIFFRACTION100
2.42-2.670.20641460.16278581X-RAY DIFFRACTION99.97
2.67-3.050.21691430.16398582X-RAY DIFFRACTION100
3.05-3.840.20781470.15318680X-RAY DIFFRACTION99.98
3.84-30.610.17691510.15078962X-RAY DIFFRACTION99.48

+
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