[English] 日本語
Yorodumi
- PDB-1i2d: CRYSTAL STRUCTURE OF ATP SULFURYLASE FROM PENICILLIUM CHRYSOGENUM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i2d
TitleCRYSTAL STRUCTURE OF ATP SULFURYLASE FROM PENICILLIUM CHRYSOGENUM
ComponentsATP SULFURYLASE
KeywordsTRANSFERASE / nucleotide binding / allosteric / hexamer
Function / homology
Function and homology information


sulfur amino acid metabolic process / sulfate assimilation via adenylyl sulfate reduction / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate kinase ...Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate kinase / PUA-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-PHOSPHOSULFATE / Sulfate adenylyltransferase
Similarity search - Component
Biological speciesPenicillium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.81 Å
AuthorsMacRae, I.J. / Segel, I.H. / Fisher, A.J.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of ATP sulfurylase from Penicillium chrysogenum: insights into the allosteric regulation of sulfate assimilation.
Authors: MacRae, I.J. / Segel, I.H. / Fisher, A.J.
History
DepositionFeb 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP SULFURYLASE
B: ATP SULFURYLASE
C: ATP SULFURYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,7099
Polymers192,1453
Non-polymers2,5646
Water5,080282
1
A: ATP SULFURYLASE
B: ATP SULFURYLASE
C: ATP SULFURYLASE
hetero molecules

A: ATP SULFURYLASE
B: ATP SULFURYLASE
C: ATP SULFURYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,41818
Polymers384,2916
Non-polymers5,12712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)135.670, 162.090, 273.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a hexamer generated from the trimer in the asymmetric unit by the operation: -x, -y+1, z.

-
Components

#1: Protein ATP SULFURYLASE / SULFATE ADENYLYLTRANSFERASE


Mass: 64048.469 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: APS / Plasmid: PET23A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12650, sulfate adenylyltransferase
#2: Chemical
ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O10PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsADX 574 AND 575 ARE ASSOCIATED WITH CHAIN A. ADX 576 AND 577 ARE ASSOCIATED WITH CHAIN B. ADX 578 ...ADX 574 AND 575 ARE ASSOCIATED WITH CHAIN A. ADX 576 AND 577 ARE ASSOCIATED WITH CHAIN B. ADX 578 AND 579 ARE ASSOCIATED WITH CHAIN C.
Sequence detailsTHE SEQUENCE/SEQUENCE DATABASE CONFLICT IS DUE TO AN ERROR IN THE DATABASE SEQUENCE. THE AUTHORS ...THE SEQUENCE/SEQUENCE DATABASE CONFLICT IS DUE TO AN ERROR IN THE DATABASE SEQUENCE. THE AUTHORS HAVE SEQUENCED THE GENE 4 TIMES AND DETERMINED THAT RESIDUE 100 IS A GLY, NOT ALA.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 M sodium citrate, 2% PEG 400, 100 mM Tris-Cl, 5 mM adenosine 5'-phosphosulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 69 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Msodium citrate1reservoir
22-4 %ethylene glycol1reservoir
35 mMAPS1reservoir
4100 mMTris-Cl1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2000
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 75367 / Num. obs: 75367 / % possible obs: 95.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 60.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5681 / % possible all: 73
Reflection
*PLUS
Num. measured all: 257680

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.81→29.08 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2928114.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Non-crystallographic symmetry was tightly imposed. CYS 42 is the only CYS that appears to have HG bound.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3650 5.1 %RANDOM
Rwork0.207 ---
obs0.207 71486 97.5 %-
all-75136 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.04 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 65.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.2 Å20 Å20 Å2
2--6.99 Å20 Å2
3----1.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.81→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13407 0 162 282 13851
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_mcbond_it3.471.5
X-RAY DIFFRACTIONc_mcangle_it5.232
X-RAY DIFFRACTIONc_scbond_it5.342
X-RAY DIFFRACTIONc_scangle_it7.322.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 521 4.9 %
Rwork0.323 10156 -
obs-10677 87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMAPS.TOP
X-RAY DIFFRACTION3APS.PARATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 65.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.382 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.323

+
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://pdbjlvh1.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