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- PDB-7cnr: Crystal structure of Thermococcus kodakaraensis aconitase X (apo-form) -

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Basic information

Entry
Database: PDB / ID: 7cnr
TitleCrystal structure of Thermococcus kodakaraensis aconitase X (apo-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 / Phosphomevalonate dehydratase large subunit / Phosphomevalonate dehydratase small subunit
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.39 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
C: DUF521 domain-containing protein
D: UPF0107 protein TK1248
E: DUF521 domain-containing protein
F: UPF0107 protein TK1248
G: DUF521 domain-containing protein
H: UPF0107 protein TK1248
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,46112
Polymers225,2778
Non-polymers1,1834
Water00
1
A: DUF521 domain-containing protein
B: UPF0107 protein TK1248
C: DUF521 domain-containing protein
D: UPF0107 protein TK1248
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2306
Polymers112,6394
Non-polymers5922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-83 kcal/mol
Surface area37330 Å2
MethodPISA
2
E: DUF521 domain-containing protein
F: UPF0107 protein TK1248
G: DUF521 domain-containing protein
H: UPF0107 protein TK1248
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2306
Polymers112,6394
Non-polymers5922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-81 kcal/mol
Surface area37100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.720, 141.720, 278.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
DUF521 domain-containing protein


Mass: 42410.320 Da / Num. of mol.: 4
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.: 4
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-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.39→49.312 Å / Num. obs: 74870 / % possible obs: 99.7 % / Redundancy: 6.648 % / Biso Wilson estimate: 85.829 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.187 / Rrim(I) all: 0.203 / Χ2: 1.187 / Net I/σ(I): 9.51 / Num. measured all: 497752
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
3.39-3.596.4791.2631.397693712058118740.5741.37398.5
3.59-3.846.7060.7972.297651211410114100.7730.865100
3.84-4.156.8920.4913.787291010580105790.9070.531100
4.15-4.546.6570.2936.2264879974897460.9650.318100
4.54-5.076.7170.2078.8259441884988490.9810.225100
5.07-5.846.7220.1919.5452223776977690.9830.207100
5.84-7.136.730.11815.0844520661666150.9950.128100
7.13-9.986.3830.04933.7632648511551150.9990.053100
9.98-49.3126.070.02749.6117682294329130.9990.0399

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.39→23.288 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 2001 5.02 %
Rwork0.1819 37873 -
obs0.1841 39874 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.01 Å2 / Biso mean: 94.9341 Å2 / Biso min: 52.01 Å2
Refinement stepCycle: final / Resolution: 3.39→23.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15715 0 28 0 15743
Biso mean--119.81 --
Num. residues----2063
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.39-3.47420.29761200.2769258197
3.4742-3.56780.34041510.26962652100
3.5678-3.67240.34191280.24922674100
3.6724-3.79050.33741350.23262675100
3.7905-3.92530.28811450.22072678100
3.9253-4.08170.25411550.20352650100
4.0817-4.26640.23661430.17682703100
4.2664-4.48980.23371490.17132669100
4.4898-4.76890.19551550.15822694100
4.7689-5.13340.21481350.15982725100
5.1334-5.64340.22221440.1682719100
5.6434-6.44480.23021460.18252753100
6.4448-8.06340.18881350.16622787100
8.0634-23.2880.17151600.15042913100

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