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- PDB-6p35: 2.5 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate re... -

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Basic information

Entry
Database: PDB / ID: 6p35
Title2.5 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with 2-keto arginine and NADP
ComponentsGlyoxylate/hydroxypyruvate reductase A
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


glycerate dehydrogenase activity / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol / cytoplasm
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 5-[(diaminomethylidene)amino]-2-oxopentanoic acid / Glyoxylate/hydroxypyruvate reductase A / Glyoxylate/hydroxypyruvate reductase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 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 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 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)36,9199
Polymers35,3571
Non-polymers1,5628
Water2,234124
1
A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules

A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,83918
Polymers70,7152
Non-polymers3,12416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area8700 Å2
ΔGint-101 kcal/mol
Surface area25640 Å2
MethodPISA
2
A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules

A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,83918
Polymers70,7152
Non-polymers3,12416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area6590 Å2
ΔGint-87 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.578, 158.578, 98.285
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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: 35357.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria)
Strain: B / BL21-DE3 / Gene: ghrA, ECBD_2566 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A140NAE3, UniProt: P75913*PLUS, glyoxylate reductase (NADP+), hydroxypyruvate reductase

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Non-polymers , 5 types, 132 molecules

#2: Chemical ChemComp-NWG / 5-[(diaminomethylidene)amino]-2-oxopentanoic acid


Mass: 173.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 5.5
Details: 17% PEG 3350, 0.2 M Li2SO4, 0.1 M BIS-TRIS pH 5.5, 1.8 mM NADP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 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: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.495→45.78 Å / Num. obs: 25774 / % possible obs: 99.7 % / Redundancy: 1.8 % / Net I/σ(I): 29.51
Reflection shellResolution: 2.495→2.584 Å / Num. unique obs: 2492

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KBO

3kbo


Resolution: 2.495→45.78 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.25
RfactorNum. reflection% reflection
Rfree0.2058 2000 7.76 %
Rwork0.1705 --
obs0.1733 25776 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.495→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 99 124 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112659
X-RAY DIFFRACTIONf_angle_d1.2093624
X-RAY DIFFRACTIONf_dihedral_angle_d19.4131575
X-RAY DIFFRACTIONf_chiral_restr0.054384
X-RAY DIFFRACTIONf_plane_restr0.008464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4952-2.55760.24761380.21991637X-RAY DIFFRACTION98
2.5576-2.62680.26161390.21911660X-RAY DIFFRACTION100
2.6268-2.70410.27721400.22321667X-RAY DIFFRACTION100
2.7041-2.79130.24961410.21441670X-RAY DIFFRACTION100
2.7913-2.89110.28221410.20841675X-RAY DIFFRACTION100
2.8911-3.00680.25891400.21131672X-RAY DIFFRACTION100
3.0068-3.14360.25151410.20251668X-RAY DIFFRACTION100
3.1436-3.30930.23991430.21171695X-RAY DIFFRACTION100
3.3093-3.51660.22091420.17051696X-RAY DIFFRACTION100
3.5166-3.7880.18061420.15261685X-RAY DIFFRACTION100
3.788-4.1690.16091430.13171712X-RAY DIFFRACTION100
4.169-4.77170.15191450.11741720X-RAY DIFFRACTION100
4.7717-6.00970.1681480.14111755X-RAY DIFFRACTION100
6.0097-45.90680.19781570.17961864X-RAY DIFFRACTION100
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)
11.658-0.2268-0.13031.24460.42071.57690.11230.221-0.1073-0.0538-0.01580.0412-0.0211-0.1985-0.08840.2371-0.0242-0.0010.38170.00170.2855-13.851764.0902-39.9641
21.2364-0.4337-0.53420.81810.05460.82590.002-0.0977-0.09280.0793-0.00060.02560.1395-0.0187-0.01530.2539-0.0618-0.01430.2773-0.00180.2607-23.143662.9196-8.0298
30.90190.9064-0.97520.9852-0.93851.09480.1195-0.14240.07830.1348-0.0534-0.0403-0.13830.2564-0.04190.30090.0043-0.00020.3497-0.0260.3407-5.724169.3494-31.1586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 281 )
3X-RAY DIFFRACTION3chain 'A' and (resid 282 through 312 )

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