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- PDB-2i9p: Crystal structure of human hydroxyisobutyrate dehydrogenase compl... -

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Basic information

Entry
Database: PDB / ID: 2i9p
TitleCrystal structure of human hydroxyisobutyrate dehydrogenase complexed with NAD+
Components3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / 3-hydroxyacid 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxyisobutyrate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKavanagh, K.L. / Papagrigoriou, E. / Salah, E. / Lukacik, P. / Smee, C. / Burgess, N. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. ...Kavanagh, K.L. / Papagrigoriou, E. / Salah, E. / Lukacik, P. / Smee, C. / Burgess, N. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human hydroxyisobutyrate dehydrogenase complexed with NAD+
Authors: Kavanagh, K.L. / Papagrigoriou, E. / Salah, E. / Lukacik, P. / Smee, C. / Burgess, N. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Oppermann, U.
History
DepositionSep 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Aug 30, 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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-hydroxyisobutyrate dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase
C: 3-hydroxyisobutyrate dehydrogenase
D: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,1218
Polymers135,4674
Non-polymers2,6544
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18650 Å2
ΔGint-157 kcal/mol
Surface area38210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.627, 167.319, 71.089
Angle α, β, γ (deg.)90.00, 107.80, 90.00
Int Tables number4
Space group name H-MP1211
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
11METMETGLNGLN2AA40 - 20623 - 189
21METMETGLNGLN2BB40 - 20623 - 189
31METMETGLNGLN2CC40 - 20623 - 189
41METMETGLNGLN2DD40 - 20623 - 189
12ALAALAGLUGLU5AA207 - 332190 - 315
22ALAALAGLUGLU5BB207 - 332190 - 315
32ALAALAGLUGLU5CC207 - 332190 - 315
42ALAALAGLUGLU5DD207 - 332190 - 315

NCS ensembles :
ID
1
2
DetailsThe biological unit is a tetramer equivalent to the asymmetric unit

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Components

#1: Protein
3-hydroxyisobutyrate dehydrogenase / HIBADH


Mass: 33866.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIBADH / Plasmid: PNIC-BSA4 (pET derivative) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P31937, 3-hydroxyisobutyrate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

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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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 24, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→62.75 Å / Num. all: 34330 / Num. obs: 34330 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.5
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.9 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GF2

2gf2


Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 26.829 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21983 1728 5 %RANDOM
Rwork0.17376 ---
all0.17616 32570 --
obs0.17616 32570 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.461 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å2-1.49 Å2
2--4.54 Å20 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8375 0 176 0 8551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228711
X-RAY DIFFRACTIONr_bond_other_d0.0020.025599
X-RAY DIFFRACTIONr_angle_refined_deg1.3522.00211835
X-RAY DIFFRACTIONr_angle_other_deg0.914313817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66251173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42125.423284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.432151362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1421523
X-RAY DIFFRACTIONr_chiral_restr0.0680.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021572
X-RAY DIFFRACTIONr_nbd_refined0.2240.22091
X-RAY DIFFRACTIONr_nbd_other0.1810.25620
X-RAY DIFFRACTIONr_nbtor_refined0.1840.24361
X-RAY DIFFRACTIONr_nbtor_other0.0890.24491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2177
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1440.28
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3910.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.71435941
X-RAY DIFFRACTIONr_mcbond_other0.49832427
X-RAY DIFFRACTIONr_mcangle_it2.65259183
X-RAY DIFFRACTIONr_scbond_it5.31473152
X-RAY DIFFRACTIONr_scangle_it7.09112651
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
11A972tight positional0.030.05
12B972tight positional0.030.05
13C972tight positional0.030.05
14D972tight positional0.030.05
11A811medium positional0.370.5
12B811medium positional0.270.5
13C811medium positional0.270.5
14D811medium positional0.280.5
21A737medium positional0.160.5
22B737medium positional0.150.5
23C737medium positional0.170.5
24D737medium positional0.130.5
21A809loose positional0.375
22B809loose positional0.395
23C809loose positional0.565
24D809loose positional0.425
11A972tight thermal0.060.5
12B972tight thermal0.070.5
13C972tight thermal0.070.5
14D972tight thermal0.070.5
11A811medium thermal0.672
12B811medium thermal0.632
13C811medium thermal0.62
14D811medium thermal0.662
21A737medium thermal0.912
22B737medium thermal0.872
23C737medium thermal0.982
24D737medium thermal0.832
21A809loose thermal2.9410
22B809loose thermal3.2410
23C809loose thermal2.7210
24D809loose thermal2.7610
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 123 -
Rwork0.289 2226 -
obs--87.62 %
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)
14.6985-0.62740.22755.946-1.07167.3309-0.2728-1.3578-0.44111.49480.00050.11260.9790.16460.27240.562-0.09730.1480.180.2017-0.0994-3.10725.05686.252
21.9537-0.223-0.68245.35531.17892.82720.1164-0.71360.19570.4964-0.1226-0.1641-0.21210.35080.0062-0.2705-0.0973-0.0275-0.0954-0.1322-0.24980.69849.31470.532
36.6285-4.0586-0.98486.08140.35984.13390.23320.28570.53520.0212-0.37790.4419-1.3742-0.73710.14460.60940.22010.1688-0.1928-0.37030.4183-16.13881.15561.863
42.1044-0.0078-0.71953.4032-0.01423.48880.1705-0.28840.06540.0176-0.48060.6859-0.2543-0.67530.3101-0.25110.03790.0107-0.0967-0.2967-0.0577-15.43151.45963.565
56.81011.2823-1.63884.2727-0.38866.28110.30330.31250.6713-1.0491-0.1507-0.6684-1.89770.8352-0.15261.0993-0.07340.4121-0.19010.34470.231311.9668.77730.054
62.5941-0.5484-0.79544.25030.86644.56020.17390.04860.067-0.3453-0.1974-0.4722-0.3530.93650.0235-0.27040.00490.0177-0.204-0.0013-0.23429.14545.10346.297
76.09132.064-0.34728.82812.63276.3445-0.21680.1356-1.0124-0.7127-0.52080.44921.6977-0.3680.73760.58050.14770.0261-0.4218-0.13840.2018-4.56211.3343.93
82.3814-0.226-0.42943.7248-0.62194.86910.12160.356-0.0957-0.6672-0.27280.4313-0.0085-0.56810.1512-0.23850.1443-0.1153-0.2819-0.1327-0.2126-6.82339.90742.273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA40 - 20623 - 189
2X-RAY DIFFRACTION2AA207 - 332190 - 315
3X-RAY DIFFRACTION3BB40 - 20623 - 189
4X-RAY DIFFRACTION4BB207 - 335190 - 318
5X-RAY DIFFRACTION5CC40 - 20623 - 189
6X-RAY DIFFRACTION6CC207 - 332190 - 315
7X-RAY DIFFRACTION7DD40 - 20623 - 189
8X-RAY DIFFRACTION8DD207 - 332190 - 315

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