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- PDB-6bii: Crystal Structure of Pyrococcus yayanosii Glyoxylate Hydroxypyruv... -

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Basic information

Entry
Database: PDB / ID: 6bii
TitleCrystal Structure of Pyrococcus yayanosii Glyoxylate Hydroxypyruvate Reductase in complex with NADP and malonate (re-refinement of 5AOW)
ComponentsGlyoxylate reductase
KeywordsOXIDOREDUCTASE / Hydroxypyruvate / Reductase / GHRB
Function / homology
Function and homology information


glyoxylate reductase / glyoxylate reductase (NADH) activity / NAD binding / cytoplasm
Similarity search - Function
Glyoxylate reductase GyaR / 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 ...Glyoxylate reductase GyaR / 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
MALONATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glyoxylate reductase
Similarity search - Component
Biological speciesPyrococcus yayanosii
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsLassalle, L. / Shabalin, I.G. / Girard, E. / Minor, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
Citation
Journal: Sci Rep / Year: 2016
Title: New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases.
Authors: Lassalle, L. / Engilberge, S. / Madern, D. / Vauclare, P. / Franzetti, B. / Girard, E.
#1: Journal: Biochemistry / Year: 2018
Title: Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
Authors: Kutner, J. / Shabalin, I.G. / Matelska, D. / Handing, K.B. / Gasiorowska, O. / Sroka, P. / Gorna, M.W. / Ginalski, K. / Wozniak, K. / Minor, W.
History
DepositionNov 2, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionJan 17, 2018ID: 5AOW
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.citation_id / _citation_author.name
Revision 1.4Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxylate reductase
B: Glyoxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,28611
Polymers75,1352
Non-polymers2,1519
Water12,791710
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-42 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.063, 141.063, 260.792
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11B-570-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 2 - 333 / Label seq-ID: 2 - 333

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Glyoxylate reductase /


Mass: 37567.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus yayanosii (strain CH1 / JCM 16557) (archaea)
Strain: CH1 / JCM 16557 / Gene: gyaR, PYCH_09300 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: F8AEA4, glyoxylate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 710 / 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

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.7 MALONATE (HAMPTON), PH 7.0. 1 ml of mother liquor was placed in the well of the crystallization plate and the drop was formed by mixing 1.5 ul of protein solution at 10 mg/ml and 1.5 ul of mother liquor
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979637 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2012 / Details: MIRROR M1
RadiationMonochromator: SI(111) DOUBLE CRISTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979637 Å / Relative weight: 1
ReflectionResolution: 2→47.97 Å / Num. obs: 103194 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 29.6 Å2 / CC1/2: 1 / Rpim(I) all: 0.062 / Rsym value: 0.17 / Net I/av σ(I): 11.7 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 14914 / CC1/2: 0.527 / Rpim(I) all: 0.683 / Rsym value: 1.88 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5AOW

5aow
PDB Unreleased entry


Resolution: 2→44.58 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 5.646 / SU ML: 0.076 / SU R Cruickshank DPI: 0.0872 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.089
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1756 5157 5 %RANDOM
Rwork0.1484 ---
obs0.1498 97977 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 216.48 Å2 / Biso mean: 41.333 Å2 / Biso min: 18.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 2→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5237 0 140 710 6087
Biso mean--37.9 50.53 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195510
X-RAY DIFFRACTIONr_bond_other_d0.0020.025327
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9957477
X-RAY DIFFRACTIONr_angle_other_deg0.969312264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76723.054239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30415944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1651549
X-RAY DIFFRACTIONr_chiral_restr0.090.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216005
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021150
Refine LS restraints NCS

Ens-ID: 1 / Number: 21184 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 369 -
Rwork0.309 7009 -
all-7378 -
obs--98.1 %
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)
12.5339-0.364-0.1844.3841.10873.35980.0016-0.25870.16070.20750.0964-0.2389-0.2220.4158-0.0980.2635-0.0166-0.04090.1485-0.03870.117283.12231.56624.349
29.89271.5697-5.61615.01112.754214.20250.07560.0880.6241-0.17420.128-0.1285-0.45040.166-0.20370.2839-0.0401-0.0470.08040.00960.151980.37442.70115.758
30.63870.0595-0.07130.65320.01380.827-0.05720.04760.03970.00490.03890.0643-0.1072-0.15920.01830.23450.0868-0.00670.0584-0.00480.063755.11321.02621.672
41.87610.51450.20451.4730.19071.6034-0.06060.16980.164-0.22150.02360.1367-0.1715-0.21840.0370.27450.1112-0.02930.11750.00820.068547.82327.43713.74
57.8505-0.6813-2.92632.0721-0.58812.59710.0253-0.13370.49240.09410.04520.0373-0.3954-0.1502-0.07050.24240.082-0.02590.0887-0.02830.080149.28533.67225.909
62.19350.0623-1.34190.58980.02752.0637-0.05920.00770.1671-0.04720.0827-0.0623-0.21550.065-0.02340.25140.0248-0.03960.0295-0.00670.050470.9727.6118.223
73.44331.84510.80545.88010.9773.2235-0.1663-0.0327-0.0132-0.0365-0.06761.1742-0.087-0.72470.23390.24610.01930.09230.39670.00510.638720.055.89638.272
83.5710.1152-0.21154.335-0.04464.7599-0.2291-0.4394-0.44410.58410.06460.68440.2701-0.43120.16460.39760.02550.21480.38770.08110.459425.671-2.48747.639
90.8749-0.3303-0.20711.45530.15120.9311-0.0316-0.0738-0.18160.09960.02180.10110.0475-0.11460.00980.2080.08080.02450.08840.01980.053850.4016.85231.386
101.2987-0.259-0.69312.20850.3472.1713-0.03040.006-0.2030.04560.02170.07570.2395-0.09630.00870.2490.06310.01580.06080.00520.115756.575-5.44332.063
1110.00871.14810.46443.1103-0.37041.84220.0281-0.6796-0.13160.4649-0.0296-0.06370.1097-0.04060.00140.26920.06940.02470.1144-0.00920.089856.5092.91844.055
122.05160.2928-0.00612.46350.20171.6229-0.13670.0669-0.38110.03120.08120.59110.2332-0.45410.05540.2590.02390.09470.19850.01110.306634.9450.635.785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 55
2X-RAY DIFFRACTION2A56 - 69
3X-RAY DIFFRACTION3A70 - 185
4X-RAY DIFFRACTION4A186 - 240
5X-RAY DIFFRACTION5A241 - 269
6X-RAY DIFFRACTION6A270 - 333
7X-RAY DIFFRACTION7B2 - 30
8X-RAY DIFFRACTION8B31 - 69
9X-RAY DIFFRACTION9B70 - 180
10X-RAY DIFFRACTION10B181 - 240
11X-RAY DIFFRACTION11B241 - 269
12X-RAY DIFFRACTION12B270 - 333

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