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- PDB-1a05: CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENA... -

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Basic information

Entry
Database: PDB / ID: 1a05
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE
Components3-ISOPROPYLMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DECARBOXYLATING DEHYDROGENASE / LEUCINE BIOSYNTHESIS
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / 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-ISOPROPYLMALIC ACID / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsImada, K. / Inagaki, K. / Matsunami, H. / Kawaguchi, H. / Tanaka, H. / Tanaka, N. / Namba, K.
Citation
Journal: Structure / Year: 1998
Title: Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism.
Authors: Imada, K. / Inagaki, K. / Matsunami, H. / Kawaguchi, H. / Tanaka, H. / Tanaka, N. / Namba, K.
#1: Journal: Biosci.Biotechnol.Biochem. / Year: 1998
Title: Overproduction and Substrate Specificity of 3-Isopropylmalate Dehydrogenase from Thiobacillus Ferrooxidans
Authors: Matsunami, H. / Kawaguchi, H. / Inagaki, K. / Eguchi, T. / Kakinuma, K. / Tanaka, H.
#2: Journal: J.Biochem.(Tokyo) / Year: 1993
Title: 3-Isopropylmalate Dehydrogenase from Chemolithoautotroph Thiobacillus Ferrooxidans: DNA Sequence, Enzyme Purification, and Characterization
Authors: Kawaguchi, H. / Inagaki, K. / Kuwata, Y. / Tanaka, H. / Tano, T.
#3: Journal: J.Ferment.Bioeng. / Year: 1990
Title: Cloning and Expression of the Thiobacillus Ferrooxidans 3-Isopropylmalate Dehydrogenase Gene in Escherichia Coli
Authors: Inagaki, K. / Kawaguchi, H. / Kuwata, Y. / Sugio, T. / Tanaka, H. / Tano, T.
History
DepositionDec 9, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-ISOPROPYLMALATE DEHYDROGENASE
B: 3-ISOPROPYLMALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4116
Polymers77,0102
Non-polymers4014
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-33 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.540, 114.240, 130.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.00211, 0.00044), (0.00211, 1, -3.0E-5), (-0.00044, -3.0E-5, -1)
Vector: 8.62482, 0.0051, 65.46259)

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Components

#1: Protein 3-ISOPROPYLMALATE DEHYDROGENASE / IPMDH / IMDH


Mass: 38505.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus ferrooxidans (bacteria)
Strain: AP19-3 / Gene: LEUB / Plasmid: PKKLEUB1 / Production host: Escherichia coli (E. coli) / Strain (production host): JA221
References: UniProt: Q56268, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IPM / 3-ISOPROPYLMALIC ACID


Mass: 176.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
210-20 %PEG60001reservoir
30.1 MMES1reservoir
420 mMIPM1reservoir
5100 mM1reservoirMgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1996 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 44212 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11
Reflection shellResolution: 2→2.25 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 3.5 / % possible all: 86
Reflection shell
*PLUS
% possible obs: 86 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
PROCESSdata reduction
PROCESSdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IPD

1ipd


Resolution: 2→8 Å / Data cutoff high absF: 550 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.275 4320 10 %RANDOM
Rwork0.1977 ---
obs0.1977 43200 75.7 %-
Displacement parametersBiso mean: 20.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-8 Å
Luzzati sigma a0.22 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5386 0 26 504 5916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.271
X-RAY DIFFRACTIONx_mcangle_it3.331
X-RAY DIFFRACTIONx_scbond_it4.026
X-RAY DIFFRACTIONx_scangle_it5.798
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.299 342 11.7 %
Rwork0.279 2918 -
obs--46.55 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.IONTOPH19.ION
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION4IPM.PARIPM.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.22

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