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Basic information

Entry
Database: PDB / ID: 1s20
TitleA novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82
ComponentsHypothetical oxidoreductase yiaK
KeywordsOXIDOREDUCTASE / alpha beta dimeric protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


3-dehydro-L-gulonate 2-dehydrogenase / 3-dehydro-L-gulonate 2-dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD+ binding / cytoplasm
Similarity search - Function
2,3-diketo-L-gulonate reductase / Hypothetical oxidoreductase yiak; domain 3 / Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain ...2,3-diketo-L-gulonate reductase / Hypothetical oxidoreductase yiak; domain 3 / Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L(+)-TARTARIC ACID / 2,3-diketo-L-gulonate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsForouhar, F. / Lee, I. / Benach, J. / Kulkarni, K. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: A Novel NAD-binding Protein Revealed by the Crystal Structure of 2,3-Diketo-L-gulonate Reductase (YiaK).
Authors: Forouhar, F. / Lee, I. / Benach, J. / Kulkarni, K. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L.
History
DepositionJan 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / struct_site
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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical oxidoreductase yiaK
B: Hypothetical oxidoreductase yiaK
C: Hypothetical oxidoreductase yiaK
D: Hypothetical oxidoreductase yiaK
E: Hypothetical oxidoreductase yiaK
F: Hypothetical oxidoreductase yiaK
G: Hypothetical oxidoreductase yiaK
H: Hypothetical oxidoreductase yiaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,96320
Polymers307,0828
Non-polymers4,88112
Water25,2391401
1
A: Hypothetical oxidoreductase yiaK
B: Hypothetical oxidoreductase yiaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3976
Polymers76,7702
Non-polymers1,6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-77 kcal/mol
Surface area23740 Å2
MethodPISA
2
C: Hypothetical oxidoreductase yiaK
D: Hypothetical oxidoreductase yiaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5844
Polymers76,7702
Non-polymers8142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-74 kcal/mol
Surface area24160 Å2
MethodPISA
3
E: Hypothetical oxidoreductase yiaK
F: Hypothetical oxidoreductase yiaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5844
Polymers76,7702
Non-polymers8142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-72 kcal/mol
Surface area23840 Å2
MethodPISA
4
G: Hypothetical oxidoreductase yiaK
H: Hypothetical oxidoreductase yiaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3976
Polymers76,7702
Non-polymers1,6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-79 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.524, 81.275, 113.215
Angle α, β, γ (deg.)79.55, 77.22, 82.01
Int Tables number1
Space group name H-MP1
Detailsdimer in both apo and complex forms

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Components

#1: Protein
Hypothetical oxidoreductase yiaK


Mass: 38385.207 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YIAK, B3575 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
References: UniProt: P37672, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1401 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 200 mM ammonium tartrate, and 20 mM NAD. The protein was pre-incubated with 10 mM 2,3-diketogulonate., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.2→24.02 Å / Num. obs: 125617 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.87 % / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.083 / Net I/σ(I): 12.29
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 4.6 / Num. unique all: 12811 / Rsym value: 0.233 / % possible all: 88.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NXU the apo enzyme

1nxu


Resolution: 2.2→24.02 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 283891.28 / Data cutoff high rms absF: 283891.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 10847 10 %RANDOM
Rwork0.191 ---
all0.19 125617 --
obs0.19 108715 83.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.3098 Å2 / ksol: 0.298138 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.42 Å23.94 Å2-4.81 Å2
2--0.75 Å2-7.64 Å2
3---2.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20633 0 324 1401 22358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 1395 9.8 %
Rwork0.22 12811 -
obs--65.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TAR.PARTAR.TOP
X-RAY DIFFRACTION4NAD.PARNAD.TOP

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