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- PDB-5tx7: Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 5tx7
TitleCrystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Desulfovibrio vulgaris
ComponentsD-isomer specific 2-hydroxyacid dehydrogenase family protein
KeywordsOXIDOREDUCTASE / NYSGRC / 2-hydroxyacid dehydrogenase / Desulfovibrio vulgaris / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / D-isomer specific 2-hydroxyacid dehydrogenase family protein
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsCzub, M.P. / Shabalin, I.G. / Gasiorowska, O.A. / Handing, K.B. / Kutner, J. / Cymborowski, M.T. / Hennig, P.M. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: to be published
Title: Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Desulfovibrio vulgaris
Authors: Czub, M.P. / Shabalin, I.G. / Gasiorowska, O.A. / Handing, K.B. / Kutner, J. / Cymborowski, M.T. / Hennig, P.M. / Bonanno, J. / Almo, S.C. / Minor, W.
History
DepositionNov 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references / Structure summary
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-isomer specific 2-hydroxyacid dehydrogenase family protein
B: D-isomer specific 2-hydroxyacid dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6945
Polymers70,3322
Non-polymers3623
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-20 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.109, 117.107, 135.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-669-

HOH

31B-537-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 1 - 321 / Label seq-ID: 2 - 322

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein D-isomer specific 2-hydroxyacid dehydrogenase family protein


Mass: 35165.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Gene: AAS95890.1 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q72C72, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 ul of 19 mg/ml protein in 50 mM Tris pH 7.5, 300 mM NaCl, and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG II condition #21 (1M Ammonium Sulfate, 0.1M Bis-Tris, 1%w/v PEG 3350 pH=5.5) ...Details: 0.2 ul of 19 mg/ml protein in 50 mM Tris pH 7.5, 300 mM NaCl, and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG II condition #21 (1M Ammonium Sulfate, 0.1M Bis-Tris, 1%w/v PEG 3350 pH=5.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/15 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2014
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.5→50.01 Å / Num. obs: 25228 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 57.1 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/av σ(I): 19.175 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2% possible all
2.5-2.545.20.772.5312690.666100
2.54-2.595.40.6480.748100
2.59-2.645.30.5690.789100
2.64-2.695.30.4980.858100
2.69-2.755.30.4140.876100
2.75-2.825.30.370.903100
2.82-2.895.30.3410.918100
2.89-2.965.30.2810.934100
2.96-3.055.30.2170.962100
3.05-3.155.30.1850.966100
3.15-3.265.30.1520.979100
3.26-3.395.30.1260.986100
3.39-3.555.20.1020.989100
3.55-3.735.30.0840.99299.9
3.73-3.975.20.0730.994100
3.97-4.275.20.0640.995100
4.27-4.75.20.0560.99699.9
4.7-5.385.10.0560.99599.8
5.38-6.785.10.0520.99699.8
6.78-504.90.0580.99499

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CUK

2cuk


Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.721 / SU ML: 0.213 / SU R Cruickshank DPI: 0.5182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.518 / ESU R Free: 0.27
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 1240 4.9 %RANDOM
Rwork0.1739 ---
obs0.1768 23947 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 170.71 Å2 / Biso mean: 68.79 Å2 / Biso min: 28.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0 Å2
2--1.35 Å20 Å2
3----2.08 Å2
Refinement stepCycle: final / Resolution: 2.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4743 0 24 291 5058
Biso mean--79.79 58.8 -
Num. residues----645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194870
X-RAY DIFFRACTIONr_bond_other_d0.0020.024619
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9626654
X-RAY DIFFRACTIONr_angle_other_deg0.944310575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1095643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79423.152184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73815700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6751535
X-RAY DIFFRACTIONr_chiral_restr0.0740.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021065
X-RAY DIFFRACTIONr_mcbond_it1.7473.6582578
X-RAY DIFFRACTIONr_mcbond_other1.7473.6582577
X-RAY DIFFRACTIONr_mcangle_it2.7665.4863219
Refine LS restraints NCS

Ens-ID: 1 / Number: 18828 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.508→2.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 88 -
Rwork0.247 1724 -
all-1812 -
obs--97.84 %
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)
12.261-0.5857-1.7472.45080.63093.7565-0.06020.472-0.149-0.3058-0.16030.18360.0301-0.10780.22050.133-0.0277-0.03280.1491-0.06770.1694.49630.92447.65
22.71460.03770.91131.44281.02242.99370.0067-0.6057-0.18670.4006-0.1419-0.05610.3397-0.42220.13520.2453-0.05570.00510.15830.04210.13819.06337.93882.565
36.1289-2.5837-0.35835.9221.37652.0463-0.02260.55990.5988-0.487-0.1641-0.5367-0.47190.25340.18680.2009-0.0782-0.00720.11890.10180.210132.10744.75467.725
46.5976-1.34132.28312.5669-1.30565.3970.23940.4544-0.398-0.2736-0.1242-0.08670.58960.2887-0.11520.14610.02950.02240.0352-0.02430.203731.50528.14968.958
52.91610.32291.45660.83030.59312.31930.04010.1818-0.2093-0.1796-0.0307-0.01710.10760.0795-0.00940.1843-0.02170.02770.029-0.03480.187114.84333.17660.399
63.53770.3176-0.49755.35760.10252.1789-0.1892-0.41060.46910.74720.09090.3442-0.3499-0.18770.09830.50490.1684-0.08250.3753-0.0340.197925.16948.889111.272
73.77751.69672.77083.53720.87433.1375-0.1591-0.53250.24950.1756-0.24320.358-0.215-0.59320.40230.13980.03880.03270.1314-0.05760.147812.88641.88677.243
810.84513.7704-1.14995.5138-3.179310.0573-1.014-0.63491.94750.2689-0.05770.934-1.779-0.65931.07160.83250.2893-0.35180.1411-0.27580.83859.64862.79579.89
97.8358-0.6407-2.50073.7538-0.36031.2498-0.0008-0.92450.75590.7264-0.00710.9036-0.1668-0.21910.00790.39970.09380.10061.0157-0.62960.77741.77649.95687.562
101.65350.62750.75263.84172.08975.2299-0.2234-0.15710.54130.8232-0.09210.3418-0.0125-0.6440.31550.54920.04360.00250.409-0.0040.226319.73449.0598.95
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 96
2X-RAY DIFFRACTION2A97 - 159
3X-RAY DIFFRACTION3A160 - 208
4X-RAY DIFFRACTION4A209 - 252
5X-RAY DIFFRACTION5A253 - 322
6X-RAY DIFFRACTION6B1 - 93
7X-RAY DIFFRACTION7B94 - 174
8X-RAY DIFFRACTION8B175 - 202
9X-RAY DIFFRACTION9B203 - 264
10X-RAY DIFFRACTION10B265 - 322

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