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- PDB-2q50: Ensemble refinement of the protein crystal structure of a glyoxyl... -

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Basic information

Entry
Database: PDB / ID: 2q50
TitleEnsemble refinement of the protein crystal structure of a glyoxylate/hydroxypyruvate reductase from Homo sapiens
ComponentsGlyoxylate reductase/hydroxypyruvate reductase
KeywordsOXIDOREDUCTASE / Ensemble Refinement / Refinement Methodology Development / Q9UBQ7 / Glyoxylate reductase / hydroxypyruvate reductase / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


dicarboxylic acid metabolic process / hydroxypyruvate reductase (NADPH) activity / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / glyoxylate metabolic process / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / Glyoxylate metabolism and glycine degradation / carboxylic acid binding ...dicarboxylic acid metabolic process / hydroxypyruvate reductase (NADPH) activity / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / glyoxylate metabolic process / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / Glyoxylate metabolism and glycine degradation / carboxylic acid binding / carboxylic acid metabolic process / peroxisomal matrix / catalytic complex / NADPH binding / NAD binding / protein homodimerization activity / mitochondrion / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
: / 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 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
Glyoxylate reductase/hydroxypyruvate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.45 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 10, 2011Group: Other
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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxylate reductase/hydroxypyruvate reductase
B: Glyoxylate reductase/hydroxypyruvate reductase
C: Glyoxylate reductase/hydroxypyruvate reductase
D: Glyoxylate reductase/hydroxypyruvate reductase


Theoretical massNumber of molelcules
Total (without water)143,6064
Polymers143,6064
Non-polymers00
Water8,107450
1
A: Glyoxylate reductase/hydroxypyruvate reductase
B: Glyoxylate reductase/hydroxypyruvate reductase


Theoretical massNumber of molelcules
Total (without water)71,8032
Polymers71,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-41 kcal/mol
Surface area25770 Å2
MethodPISA, PQS
2
C: Glyoxylate reductase/hydroxypyruvate reductase
D: Glyoxylate reductase/hydroxypyruvate reductase


Theoretical massNumber of molelcules
Total (without water)71,8032
Polymers71,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-42 kcal/mol
Surface area26050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.996, 66.436, 148.774
Angle α, β, γ (deg.)90.000, 98.590, 90.000
Int Tables number4
Space group name H-MP1211
Number of models8

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Components

#1: Protein
Glyoxylate reductase/hydroxypyruvate reductase


Mass: 35901.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRHPR, GLXR, MSTP035 / Plasmid: PVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: Q9UBQ7, glyoxylate reductase (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.41 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2H1S.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 2H1S

2h1s


Resolution: 2.45→49.326 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2585741.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2h1s and the first data set in the deposited structure factor file for 2h1s ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2h1s and the first data set in the deposited structure factor file for 2h1s along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 8 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2551 5.1 %RANDOM
Rwork0.2 ---
obs0.2 50129 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.98 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å20 Å2-1.91 Å2
2---1.01 Å20 Å2
3----1.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.45→49.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9768 0 0 450 10218
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.372
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.252.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.45-2.610.3333614.90.21769840.0188885734582.7
2.61-2.810.3074125.10.20376720.0158918808490.6
2.81-3.10.3074325.20.1978800.0158916831293.2
3.1-3.540.2924685.60.19679640.0138982843293.9
3.54-4.460.2494204.80.17983790.0128998879997.8
4.46-49.30.28545850.22286990.0139165915799.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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