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- PDB-7jqj: Structure of W45F Glyoxylate/Hydroxypyruvate reductase A from Esc... -

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Basic information

Entry
Database: PDB / ID: 7jqj
TitleStructure of W45F Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with NADP+
ComponentsGlyoxylate/hydroxypyruvate reductase A
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / 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 domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glyoxylate/hydroxypyruvate reductase A
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVuksanovic, N. / Silvaggi, N.R.
CitationJournal: To Be Published
Title: Structure of W45F Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with NADP+
Authors: Vuksanovic, N. / Silvaggi, N.R.
History
DepositionAug 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7422
Polymers36,9991
Non-polymers7431
Water3,783210
1
A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules

A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4854
Polymers73,9982
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area6480 Å2
ΔGint-30 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.177, 159.177, 95.709
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
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

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Components

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


Mass: 36999.059 Da / Num. of mol.: 1 / Mutation: W45F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Gene: ghrA, ECBD_2566 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A140NAE3, glyoxylate reductase (NADP+), hydroxypyruvate reductase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.96 Å3/Da / Density % sol: 75.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 16% v/w PEG 4000, 20% v/v glycerol, 0.1 M sodium citrate pH 5.8 0.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 2.2→38.23 Å / Num. obs: 35538 / % possible obs: 97.28 % / Redundancy: 1.8 % / Biso Wilson estimate: 32.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 28.47
Reflection shellResolution: 2.204→2.283 Å / Num. unique obs: 2919 / CC1/2: 0.982

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JQH

7jqh


Resolution: 2.2→38.23 Å / SU ML: 0.1995 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1949 1763 4.96 %
Rwork0.1856 33747 -
obs0.1861 35510 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.77 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 48 210 2704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532564
X-RAY DIFFRACTIONf_angle_d1.00533506
X-RAY DIFFRACTIONf_chiral_restr0.0533383
X-RAY DIFFRACTIONf_plane_restr0.0056450
X-RAY DIFFRACTIONf_dihedral_angle_d9.09261516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.26431110.26342091X-RAY DIFFRACTION79.72
2.26-2.330.22581260.23742341X-RAY DIFFRACTION90.1
2.33-2.410.25881280.21672555X-RAY DIFFRACTION97.42
2.41-2.490.19361290.21012625X-RAY DIFFRACTION99.78
2.49-2.590.22851180.20552650X-RAY DIFFRACTION100
2.59-2.710.21091420.20322635X-RAY DIFFRACTION100
2.71-2.850.2281530.20252616X-RAY DIFFRACTION99.93
2.85-3.030.23471360.1912643X-RAY DIFFRACTION99.68
3.03-3.260.19581440.18652656X-RAY DIFFRACTION100
3.26-3.590.21321490.17992661X-RAY DIFFRACTION100
3.59-4.110.16131610.14952685X-RAY DIFFRACTION100
4.11-5.180.1341350.14752740X-RAY DIFFRACTION100
5.18-38.230.20231310.20932849X-RAY DIFFRACTION98.12
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)
13.34993690933-1.25731833012-0.8240837677685.439878435170.7365312551144.775355208920.1077716340010.517298969324-0.0843183716155-0.270339651999-0.01416784434920.245817118929-0.0871962769291-0.397104379988-0.08497099597340.149220607728-0.0363044539263-0.00315600244830.364678977275-0.01140028954750.232835811542-13.677910632664.4862862105-39.3414993631
22.51666687524-1.00684269692-0.9572420364081.036383900320.3653618699111.62130145670.0293914341254-0.271566868949-0.04546701707910.1234898248390.0217808827598-0.0395803401556-0.04419168538390.137221404425-0.05583087403790.201366487532-0.054580146423-0.01728581451110.213206289397-0.0004491710152310.199031879529-24.683282257570.7618637748-3.59106391037
34.83056423385-0.5591681883911.036356800521.15785640944-0.4008409806122.252263023020.0314579867662-0.0612890634785-0.361830183241-0.0294226421482-0.03726289930070.04785306064490.288399664405-0.0677297916188-0.00254953194990.242586950676-0.0458867484270.01725826488390.159152526381-0.01825453058310.203890857685-22.270979994858.0954368358-10.0020841247
44.166360307012.63212509822-3.496422860114.67688799856-5.711430056986.837255807980.162296962902-0.2863679654410.2709420130630.13536451566-0.122687326983-0.343360216277-0.2637099067470.5332656573790.05532472142180.265002156727-0.021085302521-0.03141005378650.269771084555-0.1242513392280.253060502595-5.9194016373569.405323682-30.7507097473
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 166 )
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 281 )
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 312 )

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