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- PDB-4f7i: Structure of Isopropylmalate dehydrogenase from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 4f7i
TitleStructure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / ISOPROPYLMALATE DEHYDROGENASE / 3-IPM-DH / BETA-IPM DEHYDROGENASE / IMDH / IPMDH
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
ETHANOL / 3-ISOPROPYLMALIC ACID / : / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPallo, A. / Graczer, E. / Zavodszky, P. / Weiss, M.S. / Vas, M.
CitationJournal: Febs J. / Year: 2014
Title: Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis.
Authors: Pallo, A. / Olah, J. / Graczer, E. / Merli, A. / Zavodszky, P. / Weiss, M.S. / Vas, M.
History
DepositionMay 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Nov 26, 2014Group: Database references
Revision 1.4Sep 4, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rsym_value
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _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)161,02261
Polymers153,5964
Non-polymers7,42757
Water7,927440
1
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,51831
Polymers76,7982
Non-polymers3,72029
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14860 Å2
ΔGint-33 kcal/mol
Surface area22700 Å2
MethodPISA
2
C: 3-isopropylmalate dehydrogenase
D: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,50430
Polymers76,7982
Non-polymers3,70628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-16 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.380, 50.720, 178.240
Angle α, β, γ (deg.)90.00, 93.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-2008-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.972637, -0.021429, 0.231342), (-0.203884, 0.556158, -0.80568), (-0.111398, -0.8308, -0.545309)32.7619, 64.55486, 54.66832

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
3-isopropylmalate dehydrogenase / 3-IPM-DH / Beta-IPM dehydrogenase / IMDH


Mass: 38398.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: leuB, TTHA1230 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)
References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase

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Non-polymers , 8 types, 497 molecules

#2: Chemical
ChemComp-IPM / 3-ISOPROPYLMALIC ACID


Mass: 176.167 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H12O5
#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-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#7: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 % PEG 6000, 10 % ethanol, 0.1 M MOPS-K pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2011
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→48 Å / Num. all: 175413 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.12 Å / Mean I/σ(I) obs: 1.92 / Num. unique all: 27157 / Rsym value: 0.42 / % possible all: 95.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y41

2y41


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.475 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19637 898 1 %RANDOM
Rwork0.15185 ---
obs0.15229 88855 99.43 %-
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: 32.392 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20.02 Å2
2--1.09 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10471 0 460 440 11371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01911258
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9932.02615281
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97151433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.11522.949434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34151777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1371596
X-RAY DIFFRACTIONr_chiral_restr0.1350.21743
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218392
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 69 -
Rwork0.212 6133 -
obs--97.96 %
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)
11.8887-0.11960.12561.52060.39912.3728-0.0835-0.1189-0.15190.08220.02930.27820.0245-0.35520.05420.02420.00310.02630.13690.03570.13955.6455-5.594127.2728
21.8155-0.20240.4521.2230.28121.4356-0.05360.01880.02690.13690.1154-0.02020.03140.0804-0.06170.01930.0237-0.00470.0509-0.00070.051729.1354-0.682720.8124
32.30560.03790.80031.2442-0.0743.091-0.1150.04330.2230.14490.0282-0.3203-0.04590.27680.08680.02750.0217-0.06070.1232-0.03890.179652.93837.131521.2706
41.67040.27550.66371.76350.34233.1804-0.07590.0029-0.1405-0.1980.0299-0.28150.04160.44630.0460.10290.01810.04610.07180.02970.108843.745-15.665965.1726
51.8970.0203-0.45380.8941-0.17811.3143-0.0701-0.0812-0.0975-0.03770.01190.04810.0386-0.02830.05820.0860.00240.00620.00610.0080.044620.3865-7.912870.1688
61.8098-0.4928-0.49541.93020.12373.9932-0.00790.0227-0.02820.0960.08140.2849-0.1719-0.8065-0.07360.08350.05950.03450.23440.02770.1384-4.1481-3.687768.5751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 99
2X-RAY DIFFRACTION1A252 - 346
3X-RAY DIFFRACTION2A100 - 251
4X-RAY DIFFRACTION2B100 - 251
5X-RAY DIFFRACTION3B0 - 99
6X-RAY DIFFRACTION3B252 - 346
7X-RAY DIFFRACTION4C0 - 99
8X-RAY DIFFRACTION4C252 - 346
9X-RAY DIFFRACTION5C100 - 251
10X-RAY DIFFRACTION5D100 - 251
11X-RAY DIFFRACTION6D0 - 99
12X-RAY DIFFRACTION6D252 - 346

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