[English] 日本語
Yorodumi
- PDB-7yq1: Crystal structure of adenosine 5'-phosphosulfate kinase from Arch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yq1
TitleCrystal structure of adenosine 5'-phosphosulfate kinase from Archaeoglobus fulgidus in complex with AMP-PNP and APS
ComponentsAdenylyl-sulfate kinase
KeywordsTRANSFERASE / APS kinase / archaea
Function / homology
Function and homology information


sulfate assimilation via adenylyl sulfate reduction / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Adenylyl-sulfate kinase / Adenylylsulphate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-PHOSPHOSULFATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / BORIC ACID / Adenylyl-sulfate kinase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsKawakami, T. / Teramoto, T. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K05384 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structure of adenosine 5'-phosphosulfate kinase isolated from Archaeoglobus fulgidus.
Authors: Kawakami, T. / Teramoto, T. / Kakuta, Y.
History
DepositionAug 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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: Adenylyl-sulfate kinase
B: Adenylyl-sulfate kinase
C: Adenylyl-sulfate kinase
D: Adenylyl-sulfate kinase
E: Adenylyl-sulfate kinase
F: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,04534
Polymers120,5596
Non-polymers6,48628
Water16,916939
1
A: Adenylyl-sulfate kinase
hetero molecules

B: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,59414
Polymers40,1862
Non-polymers2,40812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6530 Å2
ΔGint-47 kcal/mol
Surface area15620 Å2
MethodPISA
2
C: Adenylyl-sulfate kinase
hetero molecules

E: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,22610
Polymers40,1862
Non-polymers2,0398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6160 Å2
ΔGint-43 kcal/mol
Surface area15240 Å2
MethodPISA
3
D: Adenylyl-sulfate kinase
hetero molecules

F: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,22610
Polymers40,1862
Non-polymers2,0398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5990 Å2
ΔGint-44 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.230, 238.240, 132.470
Angle α, β, γ (deg.)90.00, 93.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-518-

HOH

31F-435-

HOH

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Adenylyl-sulfate kinase / APS kinase / ATP adenosine-5'-phosphosulfate 3'-phosphotransferase / Adenosine-5'-phosphosulfate kinase


Mass: 20093.211 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: cysC, XD40_0245, XD48_1780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A101DF63, adenylyl-sulfate kinase

-
Non-polymers , 6 types, 967 molecules

#2: Chemical
ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O10PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: BH3O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 1.0 M Sodium citrate tribasic, 0.1 M Sodium cacodylate-hydrochloric acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 122344 / % possible obs: 98.3 % / Redundancy: 4.3 % / CC1/2: 0.987 / Net I/σ(I): 6
Reflection shellResolution: 1.91→2.03 Å / Num. unique obs: 20197 / CC1/2: 0.587

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CB6

5cb6


Resolution: 1.91→48.48 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 1998 1.63 %
Rwork0.214 --
obs0.2146 122311 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8370 0 402 939 9711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059099
X-RAY DIFFRACTIONf_angle_d0.94412355
X-RAY DIFFRACTIONf_dihedral_angle_d19.0413501
X-RAY DIFFRACTIONf_chiral_restr0.0521323
X-RAY DIFFRACTIONf_plane_restr0.0071512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.31551250.31848443X-RAY DIFFRACTION97
1.96-2.010.30231510.2968543X-RAY DIFFRACTION97
2.01-2.070.2741420.27938491X-RAY DIFFRACTION98
2.07-2.140.33441450.27188527X-RAY DIFFRACTION98
2.14-2.210.28291370.25548523X-RAY DIFFRACTION98
2.21-2.30.2931430.24258559X-RAY DIFFRACTION98
2.3-2.410.26441500.23638571X-RAY DIFFRACTION98
2.41-2.530.24971340.23898585X-RAY DIFFRACTION98
2.53-2.690.30291400.238621X-RAY DIFFRACTION99
2.69-2.90.25281440.22178693X-RAY DIFFRACTION99
2.9-3.190.26161420.21268604X-RAY DIFFRACTION99
3.19-3.650.22181520.18628685X-RAY DIFFRACTION99
3.65-4.60.19181430.15958696X-RAY DIFFRACTION99
4.6-48.480.20211500.17258772X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -3.7133 Å / Origin y: 1.0224 Å / Origin z: 28.4662 Å
111213212223313233
T0.1079 Å2-0.0016 Å2-0.0025 Å2-0.1862 Å2-0.0078 Å2--0.1375 Å2
L0.1119 °20.0229 °2-0.0025 °2-0.0799 °2-0.015 °2--0.1487 °2
S0.0302 Å °-0.1139 Å °0.0019 Å °-0.0214 Å °-0.0337 Å °-0.0023 Å °-0.0029 Å °0.0024 Å °0.0007 Å °
Refinement TLS groupSelection details: all

+
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