[English] 日本語
Yorodumi
- PDB-1m7h: Crystal Structure of APS kinase from Penicillium Chrysogenum: Str... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m7h
TitleCrystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer
ComponentsAdenylylsulfate kinase
KeywordsTRANSFERASE / APS kinase / Adenylylsulfate kinase / sulfate metabolism / Nucleotide 2 kinase
Function / homology
Function and homology information


adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / methionine biosynthetic process / ATP binding / cytosol
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'-DIPHOSPHATE / ADENOSINE-5'-PHOSPHOSULFATE / Adenylyl-sulfate kinase
Similarity search - Component
Biological speciesPenicillium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLansdon, E.B. / Sege, I.H. / Fisher, A.J.
CitationJournal: Biochemistry / Year: 2002
Title: Ligand-Induced Structural Changes in Adenosine 5'-Phosphosulfate Kinase from Penicillium chrysogenum.
Authors: Lansdon, E.B. / Segel, I.H. / Fisher, A.J.
History
DepositionJul 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE Residue 54 in all of the subunits is listed as Arg in the database sequence (SwissProt ...SEQUENCE Residue 54 in all of the subunits is listed as Arg in the database sequence (SwissProt accession Q12657). According to the author, the gene has been resequenced and residue 54 is actually Gly.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenylylsulfate kinase
B: Adenylylsulfate kinase
C: Adenylylsulfate kinase
D: Adenylylsulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,93522
Polymers95,2194
Non-polymers3,71618
Water8,989499
1
A: Adenylylsulfate kinase
B: Adenylylsulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,56412
Polymers47,6102
Non-polymers1,95410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-108 kcal/mol
Surface area17960 Å2
MethodPISA
2
C: Adenylylsulfate kinase
D: Adenylylsulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,37210
Polymers47,6102
Non-polymers1,7628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-108 kcal/mol
Surface area17850 Å2
MethodPISA
3
A: Adenylylsulfate kinase
B: Adenylylsulfate kinase
hetero molecules

C: Adenylylsulfate kinase
D: Adenylylsulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,93522
Polymers95,2194
Non-polymers3,71618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area16120 Å2
ΔGint-246 kcal/mol
Surface area33610 Å2
MethodPISA
4
A: Adenylylsulfate kinase
B: Adenylylsulfate kinase
hetero molecules

C: Adenylylsulfate kinase
D: Adenylylsulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,93522
Polymers95,2194
Non-polymers3,71618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area16210 Å2
ΔGint-233 kcal/mol
Surface area33520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.601, 83.688, 138.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 23804.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Plasmid: pET23A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12657, adenylyl-sulfate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O10PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Na monobasic phosphate, K dibasic phosphate, succinate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris1droppH8.0
210 mg/mlprotein1drop
31.7 M1reservoirNaH2PO4
40.3 M1reservoirK2HPO4
50.1 Msodium succinate1reservoirpH4.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2002
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 621412 / Num. obs: 621412 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 9.61 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4004 / Rsym value: 0.329 / % possible all: 91.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 64678 / Num. measured all: 621412 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 91.5 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ternary structure of APS kinase

Resolution: 2→29.91 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3134 5 %RANDOM
Rwork0.215 ---
all0.217 63077 --
obs0.217 63077 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4752 Å2 / ksol: 0.369587 e/Å3
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.86 Å20 Å20 Å2
2---6.96 Å20 Å2
3----3.9 Å2
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 0 222 499 7111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 426 5 %
Rwork0.277 8173 -
obs--78.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMION.TOP
X-RAY DIFFRACTION2ION.PARAMPROTEIN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4LIGANDS.PARLIGANDS.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 64678 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

+
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