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- PDB-4kp2: Crystal structure of homoaconitase large subunit from methanococc... -

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Basic information

Entry
Database: PDB / ID: 4kp2
TitleCrystal structure of homoaconitase large subunit from methanococcus jannaschii (MJ1003)
ComponentsHomoaconitase large subunit
KeywordsLYASE / Aconitase family / alpha-beta-alpha 3-layer sandwich / Isomerase / iron-sulfur cluster binding / small subunit (MJ1271) binding
Function / homology
Function and homology information


methanogen homoaconitase / homoaconitate hydratase activity / maleate hydratase activity / 3-isopropylmalate dehydratase activity / L-leucine biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Homoaconitase/3-isopropylmalate dehydratase, large subunit / Homoaconitase/3-isopropylmalate dehydratase, large subunit, prokaryotic / 3-Isopropylmalate dehydratase, catalytic domain / : / Aconitase; domain 3 / Aconitase, domain 3 / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 / Aconitase family, 4Fe-4S cluster binding site / Aconitase, iron-sulfur domain ...Homoaconitase/3-isopropylmalate dehydratase, large subunit / Homoaconitase/3-isopropylmalate dehydratase, large subunit, prokaryotic / 3-Isopropylmalate dehydratase, catalytic domain / : / Aconitase; domain 3 / Aconitase, domain 3 / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 / Aconitase family, 4Fe-4S cluster binding site / Aconitase, iron-sulfur domain / Aconitase family (aconitate hydratase) / Aconitase family signature 1. / Aconitase family signature 2. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Methanogen homoaconitase large subunit
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.504 Å
AuthorsHwang, K.Y. / Lee, E.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase from Methanococcus jannaschii
Authors: Lee, E.H. / Lee, K. / Hwang, K.Y.
History
DepositionMay 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homoaconitase large subunit
B: Homoaconitase large subunit


Theoretical massNumber of molelcules
Total (without water)96,8552
Polymers96,8552
Non-polymers00
Water93752
1
A: Homoaconitase large subunit

B: Homoaconitase large subunit


Theoretical massNumber of molelcules
Total (without water)96,8552
Polymers96,8552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area3510 Å2
ΔGint-22 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.325, 103.098, 112.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Homoaconitase large subunit / HACN / (R)-homocitrate dehydratase / Homoaconitate hydratase / Methanogen homoaconitase


Mass: 48427.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: hacA, MJ1003 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star
References: UniProt: Q58409, EC: 4.2.1.36, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% Jeffamine ED-2001(pH7.0), 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 30, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 28145 / Num. obs: 27048 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.5-2.54191.8
2.54-2.59193.5
2.59-2.64194.2
2.64-2.69193.3
2.69-2.75194.7

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KP1

4kp1


Resolution: 2.504→46.894 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.48 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 2000 7.39 %RANDOM
Rwork0.2263 ---
obs0.23 27048 96.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.89 Å2 / Biso mean: 54.9624 Å2 / Biso min: 27.29 Å2
Refinement stepCycle: LAST / Resolution: 2.504→46.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6418 0 0 52 6470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_plane_restr0.002
X-RAY DIFFRACTIONf_chiral_restr0.038
X-RAY DIFFRACTIONf_dihedral_angle_d11.74
X-RAY DIFFRACTIONf_angle_d0.563
X-RAY DIFFRACTIONf_bond_d0.002

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