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

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Basic information

Entry
Database: PDB / ID: 7jqi
TitleStructure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with alpha-ketoglutarate and 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
2-OXOGLUTARIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glyoxylate/hydroxypyruvate reductase A
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 alpha-ketoglutarate 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

Downloads & links

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Assembly

Deposited unit
A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9283
Polymers37,0381
Non-polymers8902
Water3,765209
1
A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules

A: Glyoxylate/hydroxypyruvate reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8556
Polymers74,0762
Non-polymers1,7794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area7450 Å2
ΔGint-26 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.887, 158.887, 96.091
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-670-

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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 4.95 Å3/Da / Density % sol: 75.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 17%PEG 3350, 0.25 M Li2SO4, 1.8 mM NADP+, 0.1 M BIS TRIS pH 5.5

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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 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.399→45.87 Å / Num. obs: 28335 / % possible obs: 99.44 % / Redundancy: 2 % / Biso Wilson estimate: 34.92 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.38
Reflection shellResolution: 2.399→2.485 Å / Num. unique obs: 2727 / CC1/2: 0.973

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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: 2.4→45.87 Å / SU ML: 0.2016 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1966 1403 4.95 %
Rwork0.1585 26922 -
obs0.1603 28325 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.56 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 58 209 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092609
X-RAY DIFFRACTIONf_angle_d1.26923565
X-RAY DIFFRACTIONf_chiral_restr0.0575384
X-RAY DIFFRACTIONf_plane_restr0.0081460
X-RAY DIFFRACTIONf_dihedral_angle_d10.00141543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.21331570.172565X-RAY DIFFRACTION97.56
2.48-2.580.21331380.16662649X-RAY DIFFRACTION99.93
2.58-2.70.18281620.16012639X-RAY DIFFRACTION99.86
2.7-2.840.21711240.16672668X-RAY DIFFRACTION99.96
2.84-3.020.23031260.17882690X-RAY DIFFRACTION99.96
3.02-3.260.25811280.18032694X-RAY DIFFRACTION99.89
3.26-3.580.21381420.17082686X-RAY DIFFRACTION99.75
3.58-4.10.15271400.13982703X-RAY DIFFRACTION99.48
4.1-5.170.16861430.12672746X-RAY DIFFRACTION99.62
5.17-45.870.20021430.17192882X-RAY DIFFRACTION98.5
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)
15.24542978656-0.0316468645292-2.06482303646.82384486941.12222945866.810394918530.4541673058451.322212142680.843358527702-0.1958944697480.003802917713660.490998420739-0.96192678669-1.12671836099-0.4451402157380.3663014838990.1550449427130.03550872814360.5490509796820.1317955217960.362490155072-17.009580199872.4850083461-42.3127039348
26.278773515390.203494300610.5568937427996.306411748740.06475593478895.977511821530.1723397669940.970036301779-0.328887914301-0.4248673294080.03027297611760.2728347787240.129303601377-0.591518535444-0.1615151567490.213649401505-0.0253488842228-0.01567295119540.429241510846-0.02466680878020.261509467009-13.326360123660.9331159407-43.7492762674
32.34327976588-1.93791451954-2.921714040953.143996915531.935632495553.89380630043-0.0686075918653-0.0799963312952-0.1349527510140.1157164119030.0822632825153-0.08034303809070.1112628884010.0247628174358-0.01896690674960.201524886967-0.0133663348593-0.03767535193260.3273908382090.003564064488870.220863045998-11.143751461959.2361657434-32.4860393166
43.33035498279-0.707401676424-1.487430276061.050708967280.07778117898141.692680050080.00582538702438-0.188305065023-0.1144871917320.2268576772790.01619921532480.1365973850450.0320397905619-0.0375324504393-0.0316670912140.264986941049-0.0593616668950.01231750843230.244163574808-0.0138302978090.260496326616-28.817414749570.7208792935-2.2100978095
51.06633165541-1.15503850442-1.192025342551.29069587181.445187746471.6701761410.108977024979-0.1763884698850.2873676875540.07811919836960.0718800025087-0.384662459836-0.1489035036320.313883810398-0.1837762627230.243391216027-0.0511306540125-0.03882254067150.366640509530.005313129331520.322585776609-13.929365475370.5633485646-6.8861300761
69.60462075310.452887701057-2.112222414772.60577567965-3.02662799553.739079824250.145695124939-0.426944724244-0.2666455162160.1036010076-0.241559481246-0.09588842605530.1427373499640.4405089234810.08566210544380.235774548432-0.0272970098214-0.03304962530230.228246566901-0.002741026300510.155578518279-10.149994972360.625658544-4.98786808506
72.34475522457-1.78800829556-3.224680797594.028363819922.930577312562.06828849935-0.218417974025-0.15370438696-0.4664913117060.267701819719-0.009832060794440.09097059403360.5210174791740.02602318882020.1992818615140.255973587571-0.0414415203106-0.04358154717460.279721758560.008805755370390.305180587872-19.683699688154.5768005073-8.57983557373
83.11752723571-0.570274755816-0.8968127005582.62155911527-2.406381364952.871341649470.02649131672940.115314742714-0.321661297645-0.07468335236550.1437034385220.2849293438180.35593112688-0.241555402137-0.1434151669790.236975565471-0.0854694514769-0.01028998631770.204580199556-0.02694448340560.256358095306-28.694029729255.5238220029-12.7898505065
94.663055045780.924629571334-2.450568627484.72095147838-2.660936420064.00247666906-0.05306448853730.128853033399-0.176806835656-0.1145854367440.07394643898860.291302190660.229738528155-0.346765458223-0.02741544907250.219762560946-0.0802866540939-0.02848175446060.298192615947-0.05090442848260.19187453825-32.240855928461.9742672277-16.2127215347
102.541071558362.70975550858-3.374556486822.94930780082-3.596224876874.458929751540.166205866179-0.2112859684740.1665419446350.283866653082-0.166700427706-0.377973655916-0.2640618554090.3612856352030.01776980202640.262562859953-0.018323774312-0.01568610468980.293447587804-0.03466457998150.273003664989-5.744505150969.2775900654-30.6989433926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 94 )
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 145 )
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 166 )
6X-RAY DIFFRACTION6chain 'A' and (resid 167 through 196 )
7X-RAY DIFFRACTION7chain 'A' and (resid 197 through 224 )
8X-RAY DIFFRACTION8chain 'A' and (resid 225 through 260 )
9X-RAY DIFFRACTION9chain 'A' and (resid 261 through 281 )
10X-RAY DIFFRACTION10chain 'A' and (resid 282 through 312 )

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