[English] 日本語
Yorodumi
- PDB-1zun: Crystal Structure of a GTP-Regulated ATP Sulfurylase Heterodimer ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zun
TitleCrystal Structure of a GTP-Regulated ATP Sulfurylase Heterodimer from Pseudomonas syringae
Components
  • Sulfate adenylyltransferase subunit 2
  • sulfate adenylate transferase, subunit 1/adenylylsulfate kinase
KeywordsTRANSFERASE / beta barrel / switch domain / heterodimer / pyrophosphate / G protein / GTPase
Function / homology
Function and homology information


: / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / sulfur compound metabolic process / sulfate assimilation / hydrogen sulfide biosynthetic process / GTPase activity / GTP binding / ATP binding
Similarity search - Function
Sulphate adenylyltransferase, small subunit / Sulphate adenylyltransferase, large subunit / Sulfate adenylyltransferase subunit CysN, GTP-binding domain / Sulfate adenylyltransferase subunit CysN, Domain II / Sulfate adenylyltransferase subunit CysN, Domain III / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / Adenylyl-sulfate kinase / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors ...Sulphate adenylyltransferase, small subunit / Sulphate adenylyltransferase, large subunit / Sulfate adenylyltransferase subunit CysN, GTP-binding domain / Sulfate adenylyltransferase subunit CysN, Domain II / Sulfate adenylyltransferase subunit CysN, Domain III / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / Adenylyl-sulfate kinase / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / HUPs / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / : / Sulfate adenylyltransferase subunit 2 / Sulfate adenylyltransferase subunit 1
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
Pseudomonas syringae pv. tomato str. DC3000 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsMougous, J.D. / Lee, D.H. / Hubbard, S.C. / Schelle, M.W. / Vocadlo, D.J. / Berger, J.M. / Bertozzi, C.R.
CitationJournal: Mol.Cell / Year: 2006
Title: Molecular basis for g protein control of the prokaryotic ATP sulfurylase.
Authors: Mougous, J.D. / Lee, D.H. / Hubbard, S.C. / Schelle, M.W. / Vocadlo, D.J. / Berger, J.M. / Bertozzi, C.R.
History
DepositionMay 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfate adenylyltransferase subunit 2
B: sulfate adenylate transferase, subunit 1/adenylylsulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2326
Polymers86,2192
Non-polymers1,0144
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-54 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.072, 110.072, 171.002
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Sulfate adenylyltransferase subunit 2 / / Sulfate adenylate transferase / SAT / ATP-sulfurylase small subunit / ATP sulfurylase catalytic subunit (CysD)


Mass: 37913.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: cysD / Plasmid: pET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87WW0, sulfate adenylyltransferase
#2: Protein sulfate adenylate transferase, subunit 1/adenylylsulfate kinase / GTPase domain of ATP sulfurylase regulatory subunit (CysN)


Mass: 48304.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato str. DC3000 (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Gene: cysNC / Plasmid: pET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 28871567, UniProt: Q87WW1*PLUS

-
Non-polymers , 5 types, 91 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, tris hydrochloric acid, sodium acetate, guanosine diphosphate, 5'-adenyly-diphosphate-monothiophosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.9184, 0.9793
SYNCHROTRONALS 8.2.120.9794
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 29, 2004 / Details: MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)MADMx-ray1
2SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.97931
30.97941
ReflectionResolution: 2.7→50 Å / Num. obs: 21160 / % possible obs: 0.154 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 55.835 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 16.07
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.84 / Num. unique all: 4101 / Rsym value: 0.346 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.872 / SU B: 27.792 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 1.629 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27617 1091 5.2 %RANDOM
Rwork0.22162 ---
obs0.22439 20020 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.103 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20.64 Å20 Å2
2--1.29 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4688 0 61 87 4836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224842
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.9746558
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05623.687217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28115833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3361535
X-RAY DIFFRACTIONr_chiral_restr0.0710.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023616
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.22202
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23250
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1580.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2451.52966
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.46324775
X-RAY DIFFRACTIONr_scbond_it0.57931938
X-RAY DIFFRACTIONr_scangle_it0.9814.51783
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 59 -
Rwork0.274 1432 -
obs--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