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- PDB-2y40: Structure of Isopropylmalate dehydrogenase from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 2y40
TitleStructure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with 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-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 1.2Jul 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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9635
Polymers76,7982
Non-polymers1653
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-38.1 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.490, 112.010, 82.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.59 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7.5 / Details: 5% PEG-10000, 0.1 M HEPES PH 7.5, MICROSEEDING

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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: 2.5→99 Å / Num. obs: 27686 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 61.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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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 2Y3Z

2y3z


Resolution: 2.5→28.12 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.881 / SU B: 29.426 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R: 0.566 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29764 982 3.6 %RANDOM
Rwork0.22513 ---
obs0.22782 26513 98.23 %-
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: 63.916 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5199 0 3 71 5273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225309
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.061.9927208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6175690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.95223.019212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51115862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8721546
X-RAY DIFFRACTIONr_chiral_restr0.1350.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214042
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_it0.9741.53437
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8932.55496
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.04851872
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.996101712
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
Rfree0.41 69 -
Rwork0.381 1949 -
obs--99.31 %
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)
13.9628-0.3784-0.29593.16860.6496.3659-0.2131-0.15810.5533-0.14850.1408-0.3796-0.65750.74350.07230.2538-0.0851-0.03870.11450.05610.345413.3958-13.3287-29.6498
210.50352.1544-4.15060.6877-2.587714.94010.12260.0876-1.23560.0638-0.0541-0.0908-0.3610.1861-0.06840.4328-0.026-0.03060.4434-0.14960.606111.0835-14.926-8.3537
35.04642.3346-1.76642.0883-1.96611.9276-0.1075-0.54040.25530.0234-0.1594-0.1881-0.05080.0910.26690.19140.0809-0.02090.087-0.04630.1328-3.5789-25.8055-25.9358
44.97341.8329-0.85542.4569-1.2943.6562-0.1334-0.14790.8841-0.0130.0380.4171-0.2255-0.32910.09540.14950.0862-0.04590.0661-0.04850.2347-15.8859-23.6373-25.968
58.3335-2.7311-2.13815.96080.90352.6351-0.41940.1789-0.0431-0.1638-0.0451-0.47110.1844-0.0190.46450.1636-0.01310.0530.01820.01330.16068.7965-26.001-36.4097
64.9879-0.49210.0855.8187-0.67452.77590.0719-0.7566-0.2347-0.222-0.196-0.07360.181-0.23860.12410.1502-0.07780.060.39120.02330.1545-35.0947-54.3805-8.0195
719.4055-1.7444-10.54290.4607-0.07299.5740.0222-0.03071.08290.2209-0.0024-0.2093-1.09510.1418-0.01980.6966-0.00980.02770.4747-0.05730.5281-43.0353-35.4931-15.2194
83.95013.6322-1.30953.9781-2.36972.58550.175-1.0467-0.35230.0541-0.6724-0.49510.1067-0.17830.49730.1488-0.0108-0.01470.45610.0220.2552-17.4227-43.0227-12.8604
93.98311.4742-0.72364.0576-0.56481.95050.3668-1.5164-0.27940.4938-0.6134-0.4167-0.12880.28270.24660.1844-0.0855-0.01020.62610.14870.1405-8.7294-37.0536-5.9859
104.98271.559-0.6214.27631.9665.2694-0.1201-0.2638-0.9991-0.49-0.2328-0.57360.2825-0.22390.35290.28-0.01310.1790.18550.17390.4377-22.2525-58.3732-15.3302
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 - 346
6X-RAY DIFFRACTION6B1 - 77
7X-RAY DIFFRACTION7B78 - 84
8X-RAY DIFFRACTION8B88 - 145
9X-RAY DIFFRACTION9B150 - 250
10X-RAY DIFFRACTION10B255 - 345

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