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- PDB-2y3z: Structure of Isopropylmalate dehydrogenase from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 2y3z
TitleStructure of Isopropylmalate dehydrogenase from Thermus thermophilus - apo enzyme
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
3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 / 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 / _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

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Assembly

Deposited unit
A: 3-ISOPROPYLMALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0418
Polymers38,3991
Non-polymers1,6427
Water3,621201
1
A: 3-ISOPROPYLMALATE DEHYDROGENASE
hetero molecules

A: 3-ISOPROPYLMALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,08216
Polymers76,7982
Non-polymers3,28414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area9600 Å2
ΔGint-10.6 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.480, 76.480, 154.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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.: 1
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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPOLYETHYLENE GLYCOL (2PE): FRAGMENTS OF PEG-200

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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: 3.62 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 9 / Details: 35% PEG-550-MME, 0.1 M TRIS-HCL PH 9.0, 0.1 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.83→99 Å / Num. obs: 47324 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.7
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 91.2

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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 1HEX

1hex


Resolution: 1.83→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.53 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19698 1193 2.6 %RANDOM
Rwork0.16442 ---
obs0.16525 45360 99.27 %-
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: 32.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.83→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2632 0 82 201 2915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222809
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8522.013787
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6995350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28622.982114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40115455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1121526
X-RAY DIFFRACTIONr_chiral_restr0.1490.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212074
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_it1.1831.51757
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0342.52822
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.88651052
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.71410965
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: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 76 -
Rwork0.209 3167 -
obs--95.52 %
Refinement TLS params.Method: refined / Origin x: 18.5827 Å / Origin y: 34.5974 Å / Origin z: 18.3754 Å
111213212223313233
T0.0041 Å20.0023 Å20.0102 Å2-0.0884 Å2-0.037 Å2--0.0534 Å2
L1.2871 °20.2503 °20.6235 °2-0.4989 °20.0374 °2--1.5702 °2
S0.0128 Å °-0.0822 Å °0.0088 Å °-0.0091 Å °-0.0245 Å °-0.045 Å °-0.0111 Å °-0.045 Å °0.0117 Å °

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