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- PDB-1nxu: CRYSTAL STRUCTURE OF E. COLI HYPOTHETICAL OXIDOREDUCTASE YIAK NOR... -

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Basic information

Entry
Database: PDB / ID: 1nxu
TitleCRYSTAL STRUCTURE OF E. COLI HYPOTHETICAL OXIDOREDUCTASE YIAK NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82.
ComponentsHypothetical oxidoreductase yiaK
KeywordsSTRUCTURAL GENOMICS / OXIDOREDUCTASE / Hypothetical protein / PSI / 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
2,3-diketo-L-gulonate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsForouhar, F. / Lee, I. / Benach, J. / Kulkarni, K. / Xiao, R. / Acton, T.B. / Shastry, R. / Rost, 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
DepositionFeb 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical oxidoreductase yiaK
B: Hypothetical oxidoreductase yiaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1556
Polymers74,7702
Non-polymers3844
Water11,962664
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-145 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.012, 51.229, 108.930
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical oxidoreductase yiaK


Mass: 37385.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YIAK OR B3575 / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P37672, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / 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: 1.93 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 302 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M LiSO4, 19% PEG 3350, 1mM B-NADH, VAPOR DIFFUSION, HANGING DROP, temperature 302K, pH 7.5
Crystal grow
*PLUS
Temperature: 29 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
119 %(w/v)PEG33501reservoir
2200 mMlithium sulfate1reservoir
310 mMdithiothreitol1reservoir
416 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97896, 0.9791, 0.9200
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
20.97911
30.921
ReflectionResolution: 2→37.9 Å / Num. obs: 106854 / % possible obs: 99.3 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 3.6 % / Biso Wilson estimate: 9.6 Å2 / Rfree details: 6591 / Limit h max: 30 / Limit h min: 0 / Limit k max: 28 / Limit k min: 0 / Limit l max: 58 / Limit l min: -59 / Observed criterion F max: 34.2 / Observed criterion F min: 2.6 / Rmerge(I) obs: 0.074 / Rsym value: 0.086 / Net I/σ(I): 13.2
Reflection
*PLUS
Num. obs: 66809 / % possible obs: 99 % / Num. measured all: 312251 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.461

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→37.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2419207.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.235 7529 9.8 %RANDOM
Rwork0.192 ---
all0.2 ---
obs0.192 77015 68.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 87.6779 Å2 / ksol: 0.432992 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.21 Å20 Å2-7.33 Å2
2---1.82 Å20 Å2
3---5.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 20 664 5813
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 407 9.7 %
Rwork0.297 3773 -
obs--22.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 29 Å / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Rfactor Rfree: 0.276 / Rfactor Rwork: 0.238

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