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- PDB-1tz9: Crystal Structure of the Putative Mannonate Dehydratase from Ente... -

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Basic information

Entry
Database: PDB / ID: 1tz9
TitleCrystal Structure of the Putative Mannonate Dehydratase from Enterococcus faecalis, Northeast Structural Genomics Target EfR41
ComponentsMannonate dehydratase
KeywordsLYASE / alpha-beta protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


glucuronate catabolic process / mannonate dehydratase / mannonate dehydratase activity
Similarity search - Function
Mannonate dehydratase / D-mannonate dehydratase (UxuA) / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Mannonate dehydratase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsForouhar, F. / Chen, Y. / Xiao, R. / Cooper, B. / Shastry, R. / Acton, T.A. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative Mannonate Dehydratase from Enterococcus faecalis, Northeast Structural Genomics Target EfR41
Authors: Forouhar, F. / Chen, Y. / Xiao, R. / Cooper, B. / Shastry, R. / Acton, T.A. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannonate dehydratase
B: Mannonate dehydratase


Theoretical massNumber of molelcules
Total (without water)84,0802
Polymers84,0802
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-15 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.340, 89.941, 156.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mannonate dehydratase / D-mannonate hydrolase


Mass: 42040.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: uxuA / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82ZC9, mannonate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 10% Isopropanol, 10mM DTT, 20% PEG 4k, 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: 0.97904 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.9→29.61 Å / Num. all: 29806 / Num. obs: 29389 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.078 / Net I/σ(I): 12.21
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 4.52 / Num. unique all: 2818 / Rsym value: 0.281 / % possible all: 97

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBthen SOLVE/RESOLVEphasing
CNSrefinement
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→29.61 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2592 9.6 %RANDOM
Rwork0.221 ---
all0.225 29389 --
obs0.221 27042 90.7 %-
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å20 Å2
2---11.8 Å20 Å2
3---9.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5462 0 0 33 5495
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_angle_deg1.2
X-RAY DIFFRACTIONo_dihedral_angle_d22.5
X-RAY DIFFRACTIONo_improper_angle_d0.78
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 349 9.1 %
Rwork0.284 3494 -
obs-2818 77.7 %

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