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- PDB-3g0o: Crystal structure of 3-hydroxyisobutyrate dehydrogenase (ygbJ) fr... -

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Basic information

Entry
Database: PDB / ID: 3g0o
TitleCrystal structure of 3-hydroxyisobutyrate dehydrogenase (ygbJ) from Salmonella typhimurium
Components3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / NAD(P) / valine catabolism / tartaric acid / target 11128h / NYSGXRC / PSI-2 / Structural Genomics / Protein Structure Initiative / New York Structural GenomiX Research Consortium / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


L-threonate 2-dehydrogenase / organic acid catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding
Similarity search - Function
: / 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-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
L(+)-TARTARIC ACID / L-threonate dehydrogenase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsEswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of 3-hydroxyisobutyrate dehydrogenase (ygbJ) from Salmonella typhimurium
Authors: Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionJan 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8713
Polymers31,6851
Non-polymers1862
Water5,747319
1
A: 3-hydroxyisobutyrate dehydrogenase
hetero molecules

A: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7416
Polymers63,3702
Non-polymers3714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area4770 Å2
ΔGint-54.8 kcal/mol
Surface area20600 Å2
MethodPISA
2
A: 3-hydroxyisobutyrate dehydrogenase
hetero molecules

A: 3-hydroxyisobutyrate dehydrogenase
hetero molecules

A: 3-hydroxyisobutyrate dehydrogenase
hetero molecules

A: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,48212
Polymers126,7404
Non-polymers7428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area12260 Å2
ΔGint-113.9 kcal/mol
Surface area38480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.513, 132.416, 143.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-577-

HOH

31A-582-

HOH

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Components

#1: Protein 3-hydroxyisobutyrate dehydrogenase


Mass: 31685.031 Da / Num. of mol.: 1 / Fragment: UNP residues 3-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / Gene: ygbJ, STM2918 / Plasmid: pSGX(3) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: Q8ZMG4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.78 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M Potassium sodium tartrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 21, 2009 / Details: mirrors
RadiationMonochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 44762 / Num. obs: 44762 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.9 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.404 / Num. unique all: 2856 / % possible all: 96.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→39.4 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 102926.47 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1632 4 %RANDOM
Rwork0.207 ---
all0.231 40332 --
obs0.231 40332 89.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.9217 Å2 / ksol: 0.389036 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2--1.5 Å20 Å2
3----3.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 11 319 2367
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 214 4 %
Rwork0.299 5072 -
obs-5072 71.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4tla-param.txttla-top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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