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- PDB-7cns: Crystal structure of Thermococcus kodakaraensis aconitase X (holo... -

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Basic information

Entry
Database: PDB / ID: 7cns
TitleCrystal structure of Thermococcus kodakaraensis aconitase X (holo-form)
Components
  • DUF521 domain-containing protein
  • UPF0107 protein TK1248
KeywordsLYASE / mevalonate 5-phosphate dehydratase
Function / homology
Function and homology information


phosphomevalonate dehydratase / isopentenyl diphosphate biosynthetic process, mevalonate pathway / hydro-lyase activity / isoprenoid biosynthetic process / 4 iron, 4 sulfur cluster binding / lyase activity / metal ion binding
Similarity search - Function
Aconitase X catalytic domain, putative / Aconitase X / Aconitase X swivel domain, putative / Aconitase X subunit 2, putative / Aconitase X subunit 2, archaeal, putative / Aconitase X swivel domain
Similarity search - Domain/homology
FE3-S4 CLUSTER / Chem-PMV / Phosphomevalonate dehydratase large subunit / Phosphomevalonate dehydratase small subunit
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsMurase, Y. / Watanabe, Y. / Watanabe, S.
CitationJournal: Commun Biol / Year: 2021
Title: Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.
Authors: Watanabe, S. / Murase, Y. / Watanabe, Y. / Sakurai, Y. / Tajima, K.
History
DepositionAug 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF521 domain-containing protein
B: UPF0107 protein TK1248
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8434
Polymers56,3192
Non-polymers5242
Water4,504250
1
A: DUF521 domain-containing protein
B: UPF0107 protein TK1248
hetero molecules

A: DUF521 domain-containing protein
B: UPF0107 protein TK1248
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6878
Polymers112,6394
Non-polymers1,0484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10170 Å2
ΔGint-90 kcal/mol
Surface area34990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.444, 102.444, 115.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-773-

HOH

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Components

#1: Protein DUF521 domain-containing protein


Mass: 42410.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1249 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JGJ6
#2: Protein UPF0107 protein TK1248 / mevalonate 5-phosphate dehydratase small subunit


Mass: 13909.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JGJ7
#3: Chemical ChemComp-PMV / (3R)-3-HYDROXY-3-METHYL-5-(PHOSPHONOOXY)PENTANOIC ACID / PHOSPHOMEVALONATE


Mass: 228.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Pentaerythritol ethoxylate (15/4 EO/OH), ammonium sulfate, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.847 Å / Num. obs: 91030 / % possible obs: 98.4 % / Redundancy: 3.499 % / Biso Wilson estimate: 44.161 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Χ2: 1.343 / Net I/σ(I): 11.54 / Num. measured all: 318531
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.023.3340.8011.274761714948142810.5570.95295.5
2.02-2.163.6010.4942.395046214092140140.7790.58299.4
2.16-2.333.4620.3033.924471213076129160.9050.3698.8
2.33-2.553.5030.1796.514175312028119190.9610.21299.1
2.55-2.853.6690.11110.423989510911108750.9850.1399.7
2.85-3.293.4750.06916.9233057960395120.9930.08299.1
3.29-4.023.4420.04228.0927153810878890.9970.05197.3
4.02-5.673.5330.03137.4821753627961570.9980.03798.1
5.67-46.8473.4980.02241.512129351134670.9990.02698.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.902→46.847 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 2489 5.12 %
Rwork0.169 46088 -
obs0.1706 48577 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.81 Å2 / Biso mean: 40.699 Å2 / Biso min: 25.51 Å2
Refinement stepCycle: final / Resolution: 1.902→46.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 21 250 4208
Biso mean--36.33 44.43 -
Num. residues----517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.902-1.93860.33331320.263232492
1.9386-1.97820.27331380.2355248198
1.9782-2.02120.28951150.22672550100
2.0212-2.06820.22021380.20852548100
2.0682-2.11990.23341660.2022512100
2.1199-2.17730.23881440.18962551100
2.1773-2.24130.23231390.18382528100
2.2413-2.31370.2851190.1825255899
2.3137-2.39640.22961350.18482544100
2.3964-2.49230.23971320.17582574100
2.4923-2.60570.21151210.1724255799
2.6057-2.74310.21991510.17732558100
2.7431-2.91490.23631410.1822596100
2.9149-3.13990.23181390.18332573100
3.1399-3.45580.20521320.17572593100
3.4558-3.95570.16191490.161260699
3.9557-4.98280.15011580.13612631100
4.9828-46.8470.19521400.1562280499

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