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- PDB-2gf2: Crystal structure of human hydroxyisobutyrate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2gf2
TitleCrystal structure of human hydroxyisobutyrate dehydrogenase
Components3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase activity / L-valine catabolic process / Branched-chain amino acid catabolism / NAD binding / NADP binding / mitochondrial matrix / mitochondrion
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-hydroxyisobutyrate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsPapagrigoriou, E. / Salah, E. / Turnbull, A.P. / Smee, C. / Burgess, N. / Gileadi, O. / von Delft, F. / Gorrec, F. / Arrowsmith, C.H. / Weigelt, J. ...Papagrigoriou, E. / Salah, E. / Turnbull, A.P. / Smee, C. / Burgess, N. / Gileadi, O. / von Delft, F. / Gorrec, F. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human hydroxyisobutyrate dehydrogenase
Authors: Papagrigoriou, E. / Salah, E. / Turnbull, A.P. / Smee, C. / Burgess, N. / Gileadi, O. / von Delft, F. / Gorrec, F. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Oppermann, U.
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxyisobutyrate dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase
C: 3-hydroxyisobutyrate dehydrogenase
D: 3-hydroxyisobutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)124,6444
Polymers124,6444
Non-polymers00
Water4,918273
1
A: 3-hydroxyisobutyrate dehydrogenase
D: 3-hydroxyisobutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)62,3222
Polymers62,3222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-47 kcal/mol
Surface area22940 Å2
MethodPISA
2
B: 3-hydroxyisobutyrate dehydrogenase
C: 3-hydroxyisobutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)62,3222
Polymers62,3222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-47 kcal/mol
Surface area22090 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13620 Å2
ΔGint-124 kcal/mol
Surface area41090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.053, 122.745, 200.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILE1AA40 - 1001 - 61
21METMETILEILE1BB40 - 1001 - 61
31PROPROILEILE1CC41 - 1002 - 61
41METMETILEILE1DD40 - 1001 - 61
12THRTHRASPASP2AA101 - 29162 - 252
22THRTHRASPASP2BB101 - 29162 - 252
32THRTHRASPASP2CC101 - 29162 - 252
42THRTHRASPASP2DD101 - 29162 - 252

NCS ensembles :
ID
1
2
Detailseach biological unit compises two molecules forming a dimer. There are two biological units in the asymmetric unit; A-D and B-C

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Components

#1: Protein
3-hydroxyisobutyrate dehydrogenase / HIBADH


Mass: 31160.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIBADH / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: P31937, 3-hydroxyisobutyrate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.20M LiCl, 0.1M HEPES, 20.0% PEG 6K, 10.0% Ethylen Glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9764 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.38→48.56 Å / Num. all: 50654 / Num. obs: 50370 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.14
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.526 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→48.56 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / SU B: 15.021 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.416 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24677 2625 5.2 %RANDOM
Rwork0.20517 ---
all0.2073 50370 --
obs0.2073 47673 99.42 %-
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: 35.718 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2---1.2 Å20 Å2
3---2.84 Å2
Refinement stepCycle: LAST / Resolution: 2.38→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8491 0 0 283 8774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228627
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.98111653
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.30751174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.98725.502289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.458151466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.621523
X-RAY DIFFRACTIONr_chiral_restr0.0760.21338
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026356
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.24304
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.25997
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2401
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4891.55949
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71529198
X-RAY DIFFRACTIONr_scbond_it1.12833011
X-RAY DIFFRACTIONr_scangle_it1.8234.52453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A427tight positional0.020.05
12B427tight positional0.020.05
13C427tight positional0.010.05
14D427tight positional0.010.05
21A763tight positional0.070.05
22B763tight positional0.050.05
23C763tight positional0.040.05
24D763tight positional0.050.05
21A558medium positional0.470.5
22B558medium positional0.470.5
23C558medium positional0.430.5
24D558medium positional0.490.5
11A427tight thermal3.3610
12B427tight thermal3.1510
13C427tight thermal3.0610
14D427tight thermal2.8310
21A763tight thermal2.9110
22B763tight thermal3.2710
23C763tight thermal2.5510
24D763tight thermal2.9810
21A558medium thermal2.9210
22B558medium thermal3.0910
23C558medium thermal2.5210
24D558medium thermal2.9210
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 175 -
Rwork0.244 3384 -
obs--97.77 %

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