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- PDB-4weq: Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate r... -

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Basic information

Entry
Database: PDB / ID: 4weq
TitleCrystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in complex with NADP and sulfate
ComponentsNAD-dependent dehydrogenase
KeywordsOXIDOREDUCTASE / NADP-dependent dehydrogenase / Structural Genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


NAD binding / oxidoreductase activity
Similarity search - Function
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / NAD-dependent dehydrogenase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSroka, P. / Gasiorowska, O.A. / Handing, K.B. / Shabalin, I.G. / Osinski, T. / Hillerich, B.S. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: 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
DepositionSep 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Data collection
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3May 16, 2018Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / exptl_crystal_grow / struct
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 / _entity.details / _entity.pdbx_ec / _exptl_crystal_grow.pdbx_details / _struct.pdbx_descriptor / _struct.title
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5308
Polymers37,2641
Non-polymers1,2657
Water4,468248
1
A: NAD-dependent dehydrogenase
hetero molecules

A: NAD-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,05916
Polymers74,5292
Non-polymers2,53114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area9840 Å2
ΔGint-170 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.153, 108.153, 80.657
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-404-

SO4

21A-589-

HOH

Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NAD-dependent dehydrogenase


Mass: 37264.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein was subjected to limited proteolysis by chymotrypsin right before crystallization. Supposingly the HIS-tag was cleaved
Source: (gene. exp.) Rhizobium meliloti (bacteria) / Strain: 1021 / Gene: R00152, SMc02828, CAC41539.1 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q92T34, glyoxylate reductase (NADP+)

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Non-polymers , 6 types, 255 molecules

#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.92 Å3/Da / Density % sol: 68.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, and 5 mM NADP were mixed with 0.2 ul of the MCSG-I condition #6 (0.2 M Ammonium ...Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, and 5 mM NADP were mixed with 0.2 ul of the MCSG-I condition #6 (0.2 M Ammonium Sulfate 0.1 M Bis-Tris:HCl pH 5.5 25% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization, the protein-ligand mixture was incubated with 1/40 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours
PH range: 5.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2014
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 37017 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.021 / Rrim(I) all: 0.072 / Χ2: 1.108 / Net I/av σ(I): 41.492 / Net I/σ(I): 9.4 / Num. measured all: 452447
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0312.20.84618280.920.2520.8830.819100
2.03-2.0712.20.70318440.9530.2090.7330.833100
2.07-2.1112.30.57318020.9630.170.5980.84100
2.11-2.1512.40.46718370.9770.1390.4880.88100
2.15-2.212.30.39918350.9840.1190.4170.906100
2.2-2.2512.30.34218310.9920.1020.3570.928100
2.25-2.3112.40.3118230.9860.0920.3240.949100
2.31-2.3712.40.25518320.990.0750.2660.961100
2.37-2.4412.40.22518320.9920.0670.2340.979100
2.44-2.5212.40.1918580.9940.0560.1991.032100
2.52-2.6112.40.15418130.9950.0450.161.059100
2.61-2.7112.40.13318600.9970.0390.1391.163100
2.71-2.8412.30.10718410.9970.0320.1121.247100
2.84-2.9912.30.08818570.9980.0260.0921.316100
2.99-3.1712.20.07318470.9990.0220.0771.396100
3.17-3.4212.20.06718480.9980.020.071.465100
3.42-3.7612.10.05318830.9990.0160.0561.434100
3.76-4.3111.80.04518780.9990.0140.0471.304100
4.31-5.4311.90.04218920.9990.0130.0441.203100
5.43-5011.50.04219760.9980.0130.0451.4499.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1886 / WRfactor Rwork: 0.1534 / FOM work R set: 0.8698 / SU B: 5.645 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1059 / SU Rfree: 0.1117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.112 / SU Rfree Cruickshank DPI: 0.1117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 1769 4.8 %RANDOM
Rwork0.1543 35220 --
obs0.1561 35220 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.23 Å2 / Biso mean: 48.923 Å2 / Biso min: 30.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.44 Å20 Å2
2--0.87 Å2-0 Å2
3----2.83 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 77 250 2742
Biso mean--51.27 56.11 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192561
X-RAY DIFFRACTIONr_bond_other_d0.0060.022416
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9913492
X-RAY DIFFRACTIONr_angle_other_deg0.8435553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20323.241108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18715391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2061519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02576
X-RAY DIFFRACTIONr_mcbond_it1.8872.6761267
X-RAY DIFFRACTIONr_mcbond_other1.8872.6761266
X-RAY DIFFRACTIONr_mcangle_it2.5423.9971583
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 120 -
Rwork0.212 2550 -
all-2670 -
obs--99.7 %
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)
15.11032.5416-0.13628.05461.99384.64180.08790.03770.2452-0.0902-0.2018-0.1357-0.38010.1010.1140.1753-0.0344-0.070.21920.00870.1205-37.98431.8330.699
23.2355-0.13260.14774.8752-0.49972.75680.2180.4684-0.0014-0.0249-0.2526-0.20270.2809-0.23930.03450.0872-0.0199-0.01590.2603-0.0820.0866-42.35227.208-3.63
30.20330.23580.17790.44990.29514.06110.09960.0491-0.1460.1582-0.0644-0.04690.1549-0.349-0.03520.2189-0.146-0.07320.2501-0.08540.2056-46.14322.6397.855
41.28970.55120.43611.37380.40111.24590.0821-0.12970.05250.04090.01590.06550.0671-0.0058-0.09790.1101-0.09760.01010.2126-0.00060.1437-26.36240.74531.248
56.26073.1207-0.72972.7820.0081.3977-0.1082-0.0175-0.6116-0.06430.1588-0.15610.6579-0.1069-0.05060.3779-0.1333-0.06690.1750.06480.1822-28.72924.64532.891
61.30670.2430.47541.15830.05052.19190.0858-0.2466-0.12530.07640.05930.15540.2974-0.2556-0.14520.1283-0.14920.00490.25070.06630.1423-39.47132.80435.117
72.185-0.5712-0.02172.37021.02212.9820.0725-0.01620.1017-0.08540.01690.1789-0.0712-0.2815-0.08940.1291-0.1133-0.02020.27020.06940.2208-39.94643.01321.393
82.19750.39050.13540.1326-0.35016.31740.06840.2458-0.58370.0541-0.0443-0.11610.85480.3734-0.02410.3515-0.0785-0.05080.1661-0.0690.345-36.1816.5938.7
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 21
2X-RAY DIFFRACTION2A22 - 54
3X-RAY DIFFRACTION3A55 - 95
4X-RAY DIFFRACTION4A96 - 155
5X-RAY DIFFRACTION5A156 - 173
6X-RAY DIFFRACTION6A174 - 261
7X-RAY DIFFRACTION7A262 - 290
8X-RAY DIFFRACTION8A291 - 319

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