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- PDB-1v7l: Structure of 3-isopropylmalate isomerase small subunit from Pyroc... -

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Basic information

Entry
Database: PDB / ID: 1v7l
TitleStructure of 3-isopropylmalate isomerase small subunit from Pyrococcus horikoshii
Components3-isopropylmalate dehydratase small subunit
KeywordsLYASE / BETA BARREL
Function / homology
Function and homology information


3-isopropylmalate dehydratase / 3-isopropylmalate dehydratase activity / L-leucine 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
3-isopropylmalate dehydratase small subunit
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å
AuthorsYao, M. / Kirita, T. / Sakai, N. / Tanaka, I.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of the Pyrococcus horikoshii Isopropylmalate Isomerase Small Subunit Provides Insight into the Dual Substrate Specificity of the Enzyme
Authors: Yasutake, Y. / Yao, M. / Sakai, N. / Kirita, T. / Tanaka, I.
History
DepositionDec 18, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-isopropylmalate dehydratase small subunit
B: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)36,0682
Polymers36,0682
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 3-isopropylmalate dehydratase small subunit

A: 3-isopropylmalate dehydratase small subunit

A: 3-isopropylmalate dehydratase small subunit

A: 3-isopropylmalate dehydratase small subunit

B: 3-isopropylmalate dehydratase small subunit

B: 3-isopropylmalate dehydratase small subunit

B: 3-isopropylmalate dehydratase small subunit

B: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)144,2708
Polymers144,2708
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_565x,x-y+1,-z+1/31
crystal symmetry operation3_565-x+y,-x+1,z+1/31
crystal symmetry operation6_555x-y,x,z+1/31
crystal symmetry operation8_565x-y,-y+1,-z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area18950 Å2
ΔGint-74 kcal/mol
Surface area47870 Å2
MethodPISA
3
A: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)18,0341
Polymers18,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)18,0341
Polymers18,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.208, 95.208, 152.258
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein 3-isopropylmalate dehydratase small subunit / 3-isopropylmalate isomerase small subunit / Isopropylmalate isomerase / Alpha-IPM isomerase / IPMI


Mass: 18033.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1724 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O59393, 3-isopropylmalate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.52 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M HEPES, 1.4M AMMONIUM SULFATE, pH 7.3, 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: 1.045 / Wavelength: 0.979131, 0.979359, 0.97001
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 19, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0451
20.9791311
30.9793591
40.970011
ReflectionResolution: 1.98→25 Å / Num. all: 38097 / Num. obs: 29033 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 15.1 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.082 / Net I/σ(I): 7.1
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2 / Num. unique all: 4159 / Rsym value: 0.377 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.98→10 Å / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2914 10.1 %Random
Rwork0.206 ---
all-29033 --
obs-28757 99.8 %-
Solvent computationSolvent model: throughout / Bsol: 55.98 Å2 / ksol: 0.439 e/Å3
Displacement parametersBiso mean: 31.34 Å2
Baniso -1Baniso -2Baniso -3
1--2.903 Å2-2.555 Å20 Å2
2---2.903 Å20 Å2
3---5.805 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.296 Å0.245 Å
Luzzati d res low-5 Å
Luzzati sigma a0.197 Å0.149 Å
Refinement stepCycle: LAST / Resolution: 1.98→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 0 294 2822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_angle_deg1.64
X-RAY DIFFRACTIONc_dihedral_angle_d22.94
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it1.558
X-RAY DIFFRACTIONc_mcangle_it2.405
X-RAY DIFFRACTIONc_scbond_it2.375
X-RAY DIFFRACTIONc_scangle_it3.695
LS refinement shellResolution: 1.98→2.1 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2762 462 9.83 %
Rwork0.2352 4221 -
obs-4683 99.62 %
Xplor fileSerial no: 1 / Param file: CNS_PROTEIN_REP.PARAM / Topol file: CNS_PROTEIN.TOP

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