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- PDB-2y42: Structure of Isopropylmalate dehydrogenase from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 2y42
TitleStructure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with NADH and Mn
Components3-ISOPROPYLMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / LEUB / LEUCINE BIOSYNTHESIS
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 / 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
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGraczer, E. / merlin, A. / Singh, R.K. / Manikandan, K. / Zavodsky, P. / Weiss, M.S. / Vas, M.
Citation
Journal: Mol.Biosyst. / Year: 2011
Title: Atomic Level Description of the Domain Closure in a Dimeric Enzyme: Thermus Thermophilus 3-Isopropylmalate Dehydrogenase.
Authors: Graczer, E. / Merli, A. / Singh, R.K. / Karuppasamy, M. / Zavodszky, P. / Weiss, M.S. / Vas, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Various Enzyme-Substrate Complexes of Isopropylmalate Dehydrogenase from Thermus Thermophilus.
Authors: Merli, A. / Manikandan, K. / Graczer, E. / Schuldt, L. / Singh, R.K. / Zavodszky, P. / Vas, M. / Weiss, M.S.
History
DepositionJan 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.status_code_sf / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)157,28517
Polymers153,5964
Non-polymers3,68913
Water4,342241
1
A: 3-ISOPROPYLMALATE DEHYDROGENASE
B: 3-ISOPROPYLMALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7249
Polymers76,7982
Non-polymers1,9267
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-50.3 kcal/mol
Surface area25690 Å2
MethodPISA
2
C: 3-ISOPROPYLMALATE DEHYDROGENASE
D: 3-ISOPROPYLMALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5618
Polymers76,7982
Non-polymers1,7636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-49.6 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.380, 161.450, 83.910
Angle α, β, γ (deg.)90.00, 91.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-ISOPROPYLMALATE DEHYDROGENASE / ISOPROPYLMALATE DEHYDROGENASE / 3-IPM-DH / BETA-IPM DEHYDROGENASE / IMDH / IPMDH


Mass: 38398.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ADDITIONAL AMINO ACIDS- N-TERMINAL MAS.C- TERMINAL AAALEHHHHHH
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase
#2: Chemical
ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 9 / Details: 15% PEG-20000, 2% DIOXANE, 0.1 M BICINE PH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. obs: 51742 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y3Z

2y3z


Resolution: 2.5→19.72 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.89 / SU B: 22.297 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.637 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25422 2109 4.1 %RANDOM
Rwork0.17637 ---
obs0.17951 49505 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10542 0 235 241 11018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5632.01214966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8251400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95323.032432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65151741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4861592
X-RAY DIFFRACTIONr_chiral_restr0.0970.21688
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218310
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.56972
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3852.511139
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.32654037
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.237103827
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 151 -
Rwork0.204 3641 -
obs--99.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0126-1.5876-1.84952.2640.6293.1622-0.1922-0.40740.04370.58710.3089-0.0544-0.07790.0865-0.11670.2177-0.0052-0.0240.19810.01830.1385-3.4888-2.36926.1634
21.5274-0.18410.48590.4266-0.31992.23190.00080.22770.0472-0.1460.0164-0.0475-0.11210.0514-0.01710.0753-0.01660.01610.0411-0.00450.14376.04744.2918-7.165
31.0131-0.4916-0.70311.08810.03642.6649-0.0620.0426-0.02650.0544-0.00030.03580.1222-0.06460.06230.0170.0008-0.02190.0206-0.01250.082322.298739.5322-3.898
40.205-0.49510.48031.3124-1.05294.2757-0.0626-0.03990.03070.111-0.0161-0.0194-0.10750.00010.07870.04660.0324-0.0250.121-0.04960.140824.599141.984932.343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 999
2X-RAY DIFFRACTION2B1 - 999
3X-RAY DIFFRACTION3C0 - 999
4X-RAY DIFFRACTION4D0 - 999

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