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- PDB-2h1s: Crystal Structure of a Glyoxylate/Hydroxypyruvate reductase from ... -

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Basic information

Entry
Database: PDB / ID: 2h1s
TitleCrystal Structure of a Glyoxylate/Hydroxypyruvate reductase from Homo sapiens
ComponentsGlyoxylate reductase/hydroxypyruvate reductase
KeywordsOXIDOREDUCTASE / Q9UBQ7 / Glyoxylate reductase / hydroxypyruvate reductase / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG
Function / homology
Function and homology information


dicarboxylic acid metabolic process / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / glyoxylate metabolic process / carboxylic acid binding / Glyoxylate metabolism and glycine degradation / carboxylic acid metabolic process ...dicarboxylic acid metabolic process / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / glyoxylate metabolic process / carboxylic acid binding / Glyoxylate metabolism and glycine degradation / carboxylic acid metabolic process / peroxisomal matrix / catalytic complex / NADPH binding / NAD binding / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
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
Glyoxylate reductase/hydroxypyruvate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsBitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Crystal Structure of a Glyoxylate/Hydroxypyruvate reductase from Homo sapiens
Authors: Bitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxylate reductase/hydroxypyruvate reductase
B: Glyoxylate reductase/hydroxypyruvate reductase
C: Glyoxylate reductase/hydroxypyruvate reductase
D: Glyoxylate reductase/hydroxypyruvate reductase


Theoretical massNumber of molelcules
Total (without water)143,6064
Polymers143,6064
Non-polymers00
Water8,107450
1
A: Glyoxylate reductase/hydroxypyruvate reductase
B: Glyoxylate reductase/hydroxypyruvate reductase


Theoretical massNumber of molelcules
Total (without water)71,8032
Polymers71,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-43 kcal/mol
Surface area25990 Å2
MethodPISA
2
C: Glyoxylate reductase/hydroxypyruvate reductase
D: Glyoxylate reductase/hydroxypyruvate reductase


Theoretical massNumber of molelcules
Total (without water)71,8032
Polymers71,8032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-45 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.996, 66.436, 148.774
Angle α, β, γ (deg.)90.00, 98.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
12A
22C
13A
23C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU2AA6 - 3266 - 326
21LEULEULEULEU2BB6 - 3266 - 326
31LEULEULEULEU2DD6 - 3266 - 326
12ASPASPLEULEU2AA105 - 326105 - 326
22ASPASPLEULEU2CC105 - 326105 - 326
13LEULEUPROPRO4AA6 - 1046 - 104
23LEULEUPROPRO4CC6 - 1046 - 104

NCS ensembles :
ID
1
2
3
DetailsThe biological unit is a dimer with two biological units in the asymmetric unit (biological unit 1, chains A & B) and (biological unit 2, chains C & D)

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Components

#1: Protein
Glyoxylate reductase/hydroxypyruvate reductase


Mass: 35901.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRHPR, GLXR / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: Q9UBQ7, glyoxylate reductase (NADP+)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 MES PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (12% PEG 3350, 0.10 M MOPS PH 7). Crystal was cryo- ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 MES PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (12% PEG 3350, 0.10 M MOPS PH 7). Crystal was cryo-protected with 15% PEG 3350, 0.10 M PIPES PH 6.5 and a final concentration of 25% Ethylene glycol, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 19, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.45→49.326 Å / Num. obs: 50144 / % possible obs: 93.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.157 / Χ2: 1.34 / Net I/σ(I): 7.087
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.45-2.514.80.5042.26128321.07980.3
2.51-2.575.10.46630321.05985.4
2.57-2.645.30.42431371.10888.4
2.64-2.725.80.41132451.11190
2.72-2.86.10.37132391.20291.8
2.8-2.96.30.3233221.28493.3
2.9-3.026.40.28133241.42992.9
3.02-3.166.50.23633391.51693.1
3.16-3.336.50.20333551.61493.8
3.33-3.536.50.16633751.43595
3.53-3.816.40.1434451.47696.2
3.81-4.196.40.12435511.40698.5
4.19-4.86.60.10536011.38199.8
4.8-6.047.10.10836321.344100
6.04-807.20.09837151.33399.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å49.3 Å
Translation2.5 Å49.3 Å
Phasing dmFOM : 0.65 / FOM acentric: 0.66 / FOM centric: 0.61 / Reflection: 50129 / Reflection acentric: 47470 / Reflection centric: 2659
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7-49.3020.880.890.7824162069347
4.4-70.850.860.7472086654554
3.5-4.40.860.870.7588358360475
3.1-3.50.750.750.6885138117396
2.6-3.10.510.520.41480614203603
2.5-2.60.360.360.2683518067284

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVE2.06phasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GDH, 1WWK as a basis of 2-member ensemble

1gdh

1wwk


Resolution: 2.45→49.326 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.883 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.207 / SU B: 17.788 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.655 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 2551 5.089 %RANDOM
Rwork0.2072 ---
all0.21 ---
obs-50129 93.114 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 8.853 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-1.165 Å2
2---0.427 Å20 Å2
3---0.769 Å2
Refinement stepCycle: LAST / Resolution: 2.45→49.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9768 0 0 450 10218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229944
X-RAY DIFFRACTIONr_angle_refined_deg1.591.98113512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34451280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2623.7400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.416151700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5851580
X-RAY DIFFRACTIONr_chiral_restr0.1030.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027404
X-RAY DIFFRACTIONr_nbd_refined0.2190.24598
X-RAY DIFFRACTIONr_nbtor_refined0.3090.26788
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2525
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.217
X-RAY DIFFRACTIONr_mcbond_it0.95126571
X-RAY DIFFRACTIONr_mcangle_it1.682410288
X-RAY DIFFRACTIONr_scbond_it3.72363769
X-RAY DIFFRACTIONr_scangle_it5.649103224
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1284tight positional0.050.05
11A1158medium positional0.4650.5
11A1284tight thermal0.1340.5
11A1158medium thermal1.0152
12B1284tight positional0.0730.05
12B1158medium positional0.6070.5
12B1284tight thermal0.1440.5
12B1158medium thermal1.1852
13D1284tight positional0.0710.05
13D1158medium positional0.5410.5
13D1284tight thermal0.1360.5
13D1158medium thermal1.0482
21A888tight positional0.0650.05
21A801medium positional0.3590.5
21A888tight thermal0.1770.5
21A801medium thermal1.1452
31A753medium positional0.3510.5
31A753medium thermal0.8582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.45-2.5210.3181690.22329280.228394378.544
2.521-2.590.3071480.23931610.242386085.725
2.59-2.6650.2861740.23131750.234375689.164
2.665-2.7470.2941580.23331150.236359591.043
2.747-2.8380.3191640.21430910.22353092.21
2.838-2.9370.2741640.19730320.201342993.205
2.937-3.0480.271660.21229050.215332292.444
3.048-3.1720.2991550.21528150.219318293.338
3.172-3.3130.2731450.19927120.203305193.641
3.313-3.4750.2811710.20426100.209294094.592
3.475-3.6630.231500.19824620.2273495.538
3.663-3.8850.2511130.18824580.191265097.019
3.885-4.1530.2451250.19323270.196248798.593
4.153-4.4850.226970.18222000.184230499.696
4.485-4.9130.2141130.17920070.1812120100
4.913-5.4920.253940.20518530.2071947100
5.492-6.340.279770.23316450.2361722100
6.34-7.7620.284700.2413850.2421455100
7.762-10.9610.221580.21310970.2141155100
10.961-147.4420.318400.2746000.27665497.859
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)
15.3378-0.0196-0.29443.1171-0.53571.0977-0.06540.2432-0.528-0.3881-0.0344-0.60460.12270.04350.0999-0.0255-0.01540.075-0.0191-0.06270.0706-3.121-28.344-79.868
21.5473-0.4029-0.26221.7528-0.07531.9367-0.0303-0.2911-0.30870.29380.0287-0.26080.29370.22010.0015-0.0660.0147-0.077-0.0890.0058-0.1151-6.183-13.758-52.2
35.01640.8751.19911.84590.21661.8334-0.1354-0.12110.8641-0.0810.10480.1437-0.37070.12770.03070.0316-0.02310.0203-0.0329-0.03850.0352-21.31218.163-35.51
41.4823-0.0688-0.02131.4002-0.22071.8598-0.0110.13170.3639-0.0710.0137-0.0132-0.2955-0.0225-0.0026-0.14440.0273-0.0044-0.12240.0229-0.1754-14.215.231-63.282
55.11372.17964.13145.54943.8597.75610.8544-0.7007-0.78850.9322-0.463-0.39941.3067-0.7484-0.39140.2334-0.1759-0.17010.05250.07330.0675-0.117-56.08-9.207
61.6906-0.0307-0.31451.48710.15451.5543-0.07350.0407-0.25160.0425-0.0275-0.07580.2968-0.00330.1009-0.1153-0.0026-0.0266-0.1715-0.0031-0.186328.851-43.271-13.337
71.40160.1669-0.42714.5056-0.36834.6684-0.02620.02450.0572-0.24490.1157-0.3393-0.11360.2624-0.0895-0.048-0.01210.0463-0.1025-0.0145-0.088746.297-9.782-23.226
82.46370.3778-0.11631.9629-0.10111.31320.02050.40630.4034-0.21270.04130.1901-0.2886-0.3522-0.0618-0.0870.0239-0.0487-0.1070.038-0.107618.515-24.438-22.473
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA6 - 1056 - 105
21AA302 - 326302 - 326
32AA106 - 301106 - 301
43BB6 - 1056 - 105
53BB302 - 326302 - 326
64BB106 - 301106 - 301
75CC6 - 1056 - 105
85CC302 - 326302 - 326
96CC106 - 301106 - 301
107DD6 - 1056 - 105
117DD302 - 326302 - 326
128DD106 - 301106 - 301

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