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- PDB-3vba: Crystal structure of methanogen 3-isopropylmalate isomerase small... -

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Basic information

Entry
Database: PDB / ID: 3vba
TitleCrystal structure of methanogen 3-isopropylmalate isomerase small subunit
ComponentsIsopropylmalate/citramalate isomerase small subunit
KeywordsLYASE / LeuD / cytosol
Function / homology
Function and homology information


maleate hydratase / (R)-2-methylmalate dehydratase / (R)-2-methylmalate dehydratase activity / maleate hydratase activity / 3-isopropylmalate dehydratase / 3-isopropylmalate dehydratase activity / L-leucine biosynthetic process / isoleucine biosynthetic process
Similarity search - Function
Hydrolyase LeuD/HacB/DmdB / 3-isopropylmalate dehydratase, swivel domain / : / Aconitase; domain 4 / Aconitase, domain 4 / Aconitase A/isopropylmalate dehydratase small subunit, swivel domain / Aconitase C-terminal domain / Aconitase/3-isopropylmalate dehydratase, swivel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Isopropylmalate/citramalate isomerase small subunit
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHwang, K.Y. / Lee, E.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structure of LeuD from Methanococcus jannaschii.
Authors: Lee, E.H. / Cho, Y.W. / Hwang, K.Y.
History
DepositionJan 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Isopropylmalate/citramalate isomerase small subunit
B: Isopropylmalate/citramalate isomerase small subunit
C: Isopropylmalate/citramalate isomerase small subunit
D: Isopropylmalate/citramalate isomerase small subunit
E: Isopropylmalate/citramalate isomerase small subunit
F: Isopropylmalate/citramalate isomerase small subunit


Theoretical massNumber of molelcules
Total (without water)116,8296
Polymers116,8296
Non-polymers00
Water12,989721
1
A: Isopropylmalate/citramalate isomerase small subunit
B: Isopropylmalate/citramalate isomerase small subunit


Theoretical massNumber of molelcules
Total (without water)38,9432
Polymers38,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-11 kcal/mol
Surface area15260 Å2
MethodPISA
2
C: Isopropylmalate/citramalate isomerase small subunit
D: Isopropylmalate/citramalate isomerase small subunit


Theoretical massNumber of molelcules
Total (without water)38,9432
Polymers38,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-12 kcal/mol
Surface area14900 Å2
MethodPISA
3
E: Isopropylmalate/citramalate isomerase small subunit
F: Isopropylmalate/citramalate isomerase small subunit


Theoretical massNumber of molelcules
Total (without water)38,9432
Polymers38,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-10 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.836, 107.138, 288.714
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
Isopropylmalate/citramalate isomerase small subunit / (R)-2-methylmalate dehydratase / (R)-citramalate dehydratase / 3-isopropylmalate dehydratase / ...(R)-2-methylmalate dehydratase / (R)-citramalate dehydratase / 3-isopropylmalate dehydratase / Alpha-isopropylmalate dehydratase / Citraconate hydratase / Isopropylmalate isomerase / IPMI / Maleate hydratase / Malease


Mass: 19471.545 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: leuD, MJ1277 / Production host: Escherichia coli (E. coli)
References: UniProt: Q58673, 3-isopropylmalate dehydratase, (R)-2-methylmalate dehydratase, maleate hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 25% PEG MME 2000, 0.1M Tris-HCl , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: msc saturna200 / Detector: CCD / Date: Apr 22, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 71994 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.45 Å2
Reflection shellResolution: 1.98→2.03 Å / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.895 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8467 / SU ML: 0.26 / σ(F): 0.09 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 3571 4.96 %RANDOM
Rwork0.1968 ---
obs0.1992 71994 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.385 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 90.8 Å2 / Biso mean: 23.9456 Å2 / Biso min: 6.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.7812 Å2-0 Å20 Å2
2---1.0152 Å2-0 Å2
3---1.7964 Å2
Refinement stepCycle: LAST / Resolution: 2→43.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 0 721 8356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077767
X-RAY DIFFRACTIONf_angle_d1.0910440
X-RAY DIFFRACTIONf_chiral_restr0.0721155
X-RAY DIFFRACTIONf_plane_restr0.0051350
X-RAY DIFFRACTIONf_dihedral_angle_d15.3332986
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07150.29553550.22166673702899
2.0715-2.15440.27053380.20566797713599
2.1544-2.25250.23763420.18836828717099
2.2525-2.37120.27013620.19666694705699
2.3712-2.51980.24623650.19396751711699
2.5198-2.71430.26333560.20636829718599
2.7143-2.98740.25833580.2076856721499
2.9874-3.41950.253630.19646933729699
3.4195-4.30770.22763660.18916952731899
4.3077-43.90560.20753660.18877110747697

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