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- PDB-1xac: CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (... -

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Basic information

Entry
Database: PDB / ID: 1xac
TitleCHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (100K) STRUCTURE.
Components3-ISOPROPYLMALATE DEHYDROGENASE 2T2M6T S82R
KeywordsOXIDOREDUCTASE / CHIMERA
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Isopropylmalate dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsNagata, C. / Moriyama, H. / Tanaka, N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Cryocrystallography of 3-Isopropylmalate dehydrogenase from Thermus thermophilus and its chimeric enzyme.
Authors: Nagata, C. / Moriyama, H. / Tanaka, N. / Nakasako, M. / Yamamoto, M. / Ueki, T. / Oshima, T.
#1: Journal: To be Published
Title: The Crystal Structure of Thermostable Mutant of Chimeric 3-Isopropylmalate Dehydrogenase
Authors: Sakurai, M. / Moriyama, H. / Onodera, K. / Kadono, S. / Numata, K. / Hayashi, Y. / Kawaguchi, J. / Yamagishi, A. / Oshima, T. / Tanaka, N.
History
DepositionNov 9, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-ISOPROPYLMALATE DEHYDROGENASE 2T2M6T S82R


Theoretical massNumber of molelcules
Total (without water)37,0561
Polymers37,0561
Non-polymers00
Water4,378243
1
A: 3-ISOPROPYLMALATE DEHYDROGENASE 2T2M6T S82R

A: 3-ISOPROPYLMALATE DEHYDROGENASE 2T2M6T S82R


Theoretical massNumber of molelcules
Total (without water)74,1122
Polymers74,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4290 Å2
ΔGint-28 kcal/mol
Surface area25900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.300, 77.300, 157.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: ASN 80 - PRO 81 OMEGA = 217.92 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO 143

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Components

#1: Protein 3-ISOPROPYLMALATE DEHYDROGENASE 2T2M6T S82R / IPMDH / IMDH


Mass: 37056.246 Da / Num. of mol.: 1 / Mutation: 2T2M6T S82R
Source method: isolated from a genetically manipulated source
Details: CHIMERA IPMDH BETWEEN BACILLUS SUBTILIS (M) AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL 20% T MIDDLE 20% M RESIDUAL 60% T ORIGINAL 2T2M6T HAD BEEN MUTATED AT S82R. LOW TEMPERATURE (100K) STRUCTURE.
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: unidentified (others)
References: UniProt: P00351, UniProt: Q5SIY4*PLUS, 3-isopropylmalate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.34 %
Crystal
*PLUS
Density % sol: 67.3 %
Crystal grow
*PLUS
Temperature: 100 K / pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMHEPES11
22.2 Mammonium sulfate11
322 %(w/v)glycerol11

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Data collection

Diffraction sourceWavelength: 1.542
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 9, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionNum. obs: 22097 / % possible obs: 67.2 % / Observed criterion σ(I): 1 / Redundancy: 0.672 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
PROCESSdata reduction
X-PLORphasing
RefinementResolution: 2.1→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.2 -
obs0.2 121701
Displacement parametersBiso mean: 33.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 0 243 2855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 21701
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.51

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