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- PDB-7jqh: Structure of wild type Glyoxylate/Hydroxypyruvate reductase A fro... -

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Basic information

Entry
Database: PDB / ID: 7jqh
TitleStructure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with phosphate 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 / 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 / PHOSPHATE ION / Glyoxylate/hydroxypyruvate reductase A
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVuksanovic, N. / Silvaggi, N.R.
CitationJournal: To Be Published
Title: Structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with phosphate and 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

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Assembly

Deposited unit
A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1596
Polymers37,0381
Non-polymers1,1205
Water5,513306
1
A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules

A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,31712
Polymers74,0762
Non-polymers2,24110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area9140 Å2
ΔGint-76 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.768, 158.768, 97.699
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
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

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Components

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


Mass: 37038.098 Da / Num. of mol.: 1
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-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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 5.02 Å3/Da / Density % sol: 75.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.4M NaH2PO4/K2HPO4 pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.999→46.03 Å / Num. obs: 49378 / % possible obs: 99.95 % / Redundancy: 1.9 % / Biso Wilson estimate: 24.45 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 28.3
Reflection shellResolution: 1.999→2.07 Å / Num. unique obs: 4836 / CC1/2: 0.979 / CC star: 0.995

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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: 3KBO

3kbo


Resolution: 2→46.03 Å / SU ML: 0.1353 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.0221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1737 2000 4.05 %
Rwork0.1528 47370 -
obs0.1536 49370 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.46 Å2
Refinement stepCycle: LAST / Resolution: 2→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 69 306 2855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01442617
X-RAY DIFFRACTIONf_angle_d1.27973577
X-RAY DIFFRACTIONf_chiral_restr0.065384
X-RAY DIFFRACTIONf_plane_restr0.0101457
X-RAY DIFFRACTIONf_dihedral_angle_d8.6451539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2061390.16993314X-RAY DIFFRACTION99.68
2.05-2.10.18651410.15983306X-RAY DIFFRACTION100
2.1-2.170.18031410.15583356X-RAY DIFFRACTION100
2.17-2.240.19561400.14483321X-RAY DIFFRACTION100
2.24-2.320.1761410.13533341X-RAY DIFFRACTION100
2.32-2.410.16821420.13763344X-RAY DIFFRACTION100
2.41-2.520.16821420.14493362X-RAY DIFFRACTION99.97
2.52-2.650.17031400.14633350X-RAY DIFFRACTION100
2.65-2.820.19591430.1593362X-RAY DIFFRACTION100
2.82-3.030.21081430.16483380X-RAY DIFFRACTION100
3.03-3.340.16441430.16523397X-RAY DIFFRACTION100
3.34-3.820.15851440.1483427X-RAY DIFFRACTION100
3.82-4.820.13991470.12863465X-RAY DIFFRACTION100
4.82-46.030.19571540.17853645X-RAY DIFFRACTION99.79
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)
10.01738143006590.01970257571740.01243437822760.02051445941890.00577718085010.02034358114230.1623755443410.3521852494410.00507055567627-0.1255487408280.0205922510861-0.0175322611779-0.113324600977-0.221674302995-2.20916806534E-80.04725101503040.015877819642-0.01882914899820.3209218394330.07693837974570.112809931296-15.501403459766.7334600012-43.682831741
2-0.005708022676420.00447067162825-0.009868369865710.00461317436644-0.005059263063010.005852093106130.0001171688196340.1380301282750.03453676900370.06450526034960.04533393684080.01384060621760.0258400487511-0.03713954200356.17884858082E-80.0681818409761-0.0251439212580.002209849253060.157101614008-0.03952181136240.0965055144909-11.364967288959.0293589039-32.8571231362
30.0315930578781-0.0395584761152-0.006331907851090.1055789021520.02205388862080.01993070089580.0150085638264-0.0177379329770.01168312384490.0301500438343-0.00554240907556-0.007240399586930.04384383070740.0232707588026-2.38600570457E-90.0726955579348-0.0234256675840.006731328580080.103893652778-0.001787475256910.0830651407464-20.193563970467.9867180649-4.15367081045
40.0160816058203-0.01136720391850.01745173390710.02970178680150.0006342627325260.0126066245622-0.01455380946440.054671500032-0.1557203373510.0373612846909-0.006681858724930.08931223211160.138729953933-0.001436958806257.41044622445E-80.114872808324-0.02704649018940.01755513592260.09217391930570.008366579586370.15802772899-22.004496787154.2400352612-9.92164533391
50.003215888055-0.003891559874010.001065110425120.00498774957205-0.003721263607940.00300557908701-0.003082563153550.0372287161018-0.08059844674890.02308845962650.0272654918570.08289613277240.000695856991744-0.00723975557223-5.54568012065E-70.128955436643-0.04229576448360.007545042456080.123965986731-0.01545199225770.132349858246-30.047924735157.7732638336-13.6038994083
60.0226376741568-0.02235457510420.0005467798436550.01626874399080.002599644378860.009402807859330.0656621357782-0.00582710550159-0.00340223986432-0.0835333264507-0.08397123640780.00817144859363-0.00986343662288-0.0997720982928-2.16111804979E-70.104683092499-0.0463035676351-0.002114989572280.158717360086-0.02126793794540.124230055032-32.130030129562.0599077979-16.5446651523
7-0.000471572299256-0.00220402600333-0.0187569851115-0.000720599675307-0.01114530040340.007055117893360.0608999212420.005240448377410.0129041431510.1083705251520.07585626130440.00318983037446-0.09926274020170.004824319382661.66068191617E-70.1319322718930.007633555052320.0329884966520.1744625447990.00892807854840.164180945696-6.2610916783269.3515661551-31.1820189622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 196 )
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 241 )
5X-RAY DIFFRACTION5chain 'A' and (resid 242 through 260 )
6X-RAY DIFFRACTION6chain 'A' and (resid 261 through 281 )
7X-RAY DIFFRACTION7chain 'A' and (resid 282 through 312 )

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