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- PDB-2y41: Structure of Isopropylmalate dehydrogenase from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 2y41
TitleStructure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with IPM 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
3-ISOPROPYLMALIC ACID / : / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3708
Polymers76,7982
Non-polymers5726
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-34.2 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.240, 146.330, 175.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 2
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-IPM / 3-ISOPROPYLMALIC ACID


Mass: 176.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12O5
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7.5 / Details: 10% PEG-4000, 10% 2-PROPANOL, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→99 Å / Num. obs: 33360 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 48.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 24
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y3X

2y3x


Resolution: 2.2→28.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / SU B: 11.755 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22444 1053 3.2 %RANDOM
Rwork0.18561 ---
obs0.18682 32255 99.96 %-
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: 47.643 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5202 0 28 203 5433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225361
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.9947282
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.35696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.84822.884215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67615871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0921548
X-RAY DIFFRACTIONr_chiral_restr0.1120.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0224090
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_it0.6591.53447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1982.55518
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.98551914
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.475101761
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 66 -
Rwork0.205 2324 -
obs--99.96 %
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)
12.21530.04680.83212.3135-0.20644.57910.0309-0.12130.2617-0.043-0.03650.096-0.381-0.13080.00560.10010.02-0.0260.0586-0.04210.1644-12.1438-19.584818.4728
27.2619-2.22687.41038.79740.15018.2857-0.16680.29180.145-0.40510.1402-0.406-0.28110.37160.02660.20160.013-0.01820.0387-0.01550.0503-12.5811-33.1841.6893
31.3442-0.40520.43692.38290.16411.6057-0.0362-0.18640.01440.24170.00640.0067-0.0659-0.26370.02980.03930.0046-0.00850.0812-0.01750.0211-4.0545-37.066223.8568
41.61910.22-0.04141.91110.68333.3183-0.0047-0.2154-0.12990.2556-0.1046-0.25730.13440.26910.10930.0357-0.0038-0.0320.07410.02850.07226.3113-43.364423.2893
55.30942.0191-2.33653.5633-2.05164.73010.1131-0.27810.28290.26960.10530.4333-0.0023-0.359-0.21840.09650.01740.01710.1538-0.04750.0897-13.255-27.352531.6492
64.90250.1589-0.2313.67570.63452.46070.1846-0.3817-0.89670.223-0.1789-0.26480.51810.0658-0.00560.40220.0283-0.02870.09670.02850.34793.6367-77.309317.1851
712.1441-0.02063.662812.1136-5.72418.3642-0.0505-0.16690.46880.6296-0.2092-0.7394-0.61820.8280.25970.17640.02210.02230.19730.00040.312716.3632-59.028715.1272
80.7859-0.95070.58615.68270.68971.09620.0019-0.046-0.33870.7379-0.05030.34790.3331-0.22010.04840.1934-0.10640.1780.0974-0.16090.5146-7.0922-60.3317.7477
92.10820.15640.03492.57610.45592.1962-0.03030.1497-0.23130.0046-0.20380.45980.1829-0.47990.23420.0507-0.03880.02460.1235-0.09110.1326-13.0925-52.499210.4425
104.7751-0.4877-2.17393.0346-0.5576.4822-0.0323-1.0014-0.69890.79450.02220.41110.4830.00580.01010.4823-0.09110.14210.2730.08960.3912-7.7213-73.260925.897
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 77
2X-RAY DIFFRACTION2A78 - 84
3X-RAY DIFFRACTION3A88 - 145
4X-RAY DIFFRACTION4A150 - 250
5X-RAY DIFFRACTION5A255 - 345
6X-RAY DIFFRACTION6B1 - 77
7X-RAY DIFFRACTION7B78 - 84
8X-RAY DIFFRACTION8B88 - 145
9X-RAY DIFFRACTION9B150 - 250
10X-RAY DIFFRACTION10B255 - 345

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