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- PDB-6ovl: 2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate re... -

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Basic information

Entry
Database: PDB / ID: 6ovl
Title2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with glyoxylate and NADP
ComponentsGlyoxylate/hydroxypyruvate reductase A
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


hydroxypyruvate reductase (NADPH) activity / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / cellular response to stress / NAD binding / cytosol
Similarity search - Function
Glyoxylate/hydroxypyruvate reductase A, Enterobacterales / 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, 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
GLYOXYLIC ACID / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION / Glyoxylate/hydroxypyruvate reductase A / Glyoxylate/hydroxypyruvate reductase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVuksanovic, N. / Silvaggi, N.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: 2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with glyoxylate and NADP
Authors: Vuksanovic, N.
History
DepositionMay 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Structure summary / Category: audit_author
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3488
Polymers36,1861
Non-polymers1,1627
Water5,062281
1
A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules

A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,69616
Polymers72,3722
Non-polymers2,32314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area9670 Å2
ΔGint-63 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.820, 158.820, 96.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-722-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glyoxylate/hydroxypyruvate reductase A / 2-ketoacid reductase


Mass: 36186.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: W8T4J3, UniProt: P75913*PLUS, glyoxylate reductase (NADP+), hydroxypyruvate reductase

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Non-polymers , 7 types, 288 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O3
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.4 M sodium phosphate monobasic/ potassium phosphate dibasic, 5 mM NADP, 100 mM sodium glyoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→36.73 Å / Num. obs: 41974 / % possible obs: 99.09 % / Redundancy: 16.3 % / Biso Wilson estimate: 27.6828559215 Å2 / Net I/σ(I): 26.2
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 3924

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KBO

3kbo


Resolution: 2.1→36.73 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 2121 5.06 %
Rwork0.1636 --
obs0.1646 41937 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→36.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 71 281 2852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032637
X-RAY DIFFRACTIONf_angle_d0.6983598
X-RAY DIFFRACTIONf_dihedral_angle_d14.5961559
X-RAY DIFFRACTIONf_chiral_restr0.043385
X-RAY DIFFRACTIONf_plane_restr0.003460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.1490.27081360.22432433X-RAY DIFFRACTION93
2.149-2.20280.22931400.19162559X-RAY DIFFRACTION98
2.2028-2.26230.29061280.20732616X-RAY DIFFRACTION99
2.2623-2.32890.21841470.18452613X-RAY DIFFRACTION99
2.3289-2.4040.19061370.17492635X-RAY DIFFRACTION100
2.404-2.48990.19521640.17112612X-RAY DIFFRACTION100
2.4899-2.58960.19721350.1672637X-RAY DIFFRACTION100
2.5896-2.70740.19531400.17332650X-RAY DIFFRACTION100
2.7074-2.85010.19921430.17722671X-RAY DIFFRACTION100
2.8501-3.02860.22111240.17272674X-RAY DIFFRACTION100
3.0286-3.26230.17861360.16782690X-RAY DIFFRACTION100
3.2623-3.59040.15971400.15612691X-RAY DIFFRACTION100
3.5904-4.10930.1451590.13012675X-RAY DIFFRACTION99
4.1093-5.1750.13781350.12682760X-RAY DIFFRACTION100
5.175-36.73550.20211570.18632900X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -18.4953 Å / Origin y: 63.8768 Å / Origin z: -18.8906 Å
111213212223313233
T0.1497 Å2-0.0318 Å2-0.0124 Å2-0.1905 Å20.0009 Å2--0.2388 Å2
L1.1613 °2-0.2115 °2-0.821 °2-0.4131 °20.3023 °2--1.2802 °2
S0.0246 Å °0.1276 Å °-0.0423 Å °0.0225 Å °-0.017 Å °0.0355 Å °0.0583 Å °-0.0811 Å °-0.0092 Å °
Refinement TLS groupSelection details: all

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