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- PDB-4kp1: Crystal structure of IPM isomerase large subunit from methanococc... -

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Basic information

Entry
Database: PDB / ID: 4kp1
TitleCrystal structure of IPM isomerase large subunit from methanococcus jannaschii (MJ0499)
ComponentsIsopropylmalate/citramalate isomerase large subunit
KeywordsISOMERASE / Aconitase family / alpha-beta-alpha 3-layer sandwich / iron-sulfur cluster binding / small subunit (MJ1277) binding
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 / 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
2,4-dimethylpentane-2,4-diol / Isopropylmalate/citramalate isomerase large subunit
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isopropylmalate/citramalate isomerase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8477
Polymers49,2181
Non-polymers6296
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.457, 98.838, 142.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-750-

HOH

21A-753-

HOH

31A-768-

HOH

41A-810-

HOH

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Components

#1: Protein Isopropylmalate/citramalate isomerase large 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: 49217.941 Da / Num. of mol.: 1
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: leuC, MJ0499 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star
References: UniProt: P81291, 3-isopropylmalate dehydratase, (R)-2-methylmalate dehydratase
#2: Chemical ChemComp-KP1 / 2,4-dimethylpentane-2,4-diol


Mass: 132.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O2
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.7
Details: 60% MPD, 0.1M Bicine, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2010
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 51020 / Num. obs: 50087 / % possible obs: 98.17 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.8-1.86195.7
1.86-1.91196.5
1.91-1.97197.2
1.97-2.03198
2.03-2.1198.4

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→34.036 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.48 / σ(F): 1.49 / Phase error: 31.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 2558 5.11 %
Rwork0.2148 --
obs0.2167 50087 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.6163 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 42 212 3475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123318
X-RAY DIFFRACTIONf_angle_d1.3844485
X-RAY DIFFRACTIONf_dihedral_angle_d16.6471227
X-RAY DIFFRACTIONf_chiral_restr0.084511
X-RAY DIFFRACTIONf_plane_restr0.006572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83460.47511420.42832511X-RAY DIFFRACTION95
1.8346-1.8720.36361360.39782541X-RAY DIFFRACTION96
1.872-1.91270.39161410.37022566X-RAY DIFFRACTION97
1.9127-1.95720.3631230.35552612X-RAY DIFFRACTION97
1.9572-2.00620.39721570.32972582X-RAY DIFFRACTION98
2.0062-2.06040.35041470.32362633X-RAY DIFFRACTION99
2.0604-2.1210.31571250.2832628X-RAY DIFFRACTION98
2.121-2.18950.32091540.26792613X-RAY DIFFRACTION98
2.1895-2.26770.25151340.24662639X-RAY DIFFRACTION98
2.2677-2.35850.30031700.21972589X-RAY DIFFRACTION99
2.3585-2.46580.25831460.21612651X-RAY DIFFRACTION99
2.4658-2.59580.24211340.19922685X-RAY DIFFRACTION99
2.5958-2.75830.30021520.19662668X-RAY DIFFRACTION100
2.7583-2.97120.27021420.19742689X-RAY DIFFRACTION99
2.9712-3.270.23161450.18822681X-RAY DIFFRACTION99
3.27-3.74260.22141290.17272717X-RAY DIFFRACTION99
3.7426-4.71330.1821420.15452735X-RAY DIFFRACTION99
4.7133-34.04250.19041390.18572789X-RAY DIFFRACTION97

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