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- PDB-3ojo: Derivative structure of the UDP-N-acetyl-mannosamine dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 3ojo
TitleDerivative structure of the UDP-N-acetyl-mannosamine dehydrogenase Cap5O from S. aureus
ComponentsCap5O
KeywordsOXIDOREDUCTASE / Rossmann fold / complex with cofactor NAD and Eu(PDC)3 / oxidized conformation
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / polysaccharide biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
UDP-N-acetyl-D-mannosamine/glucosamine dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain ...UDP-N-acetyl-D-mannosamine/glucosamine dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
EUROPIUM ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYRIDINE-2,6-DICARBOXYLIC ACID / Cap5O
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsNessler, S. / Gruszczyk, J. / Olivares-Illana, V. / Meyer, P. / Morera, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure Analysis of the Staphylococcus aureus UDP-N-acetyl-mannosamine Dehydrogenase Cap5O Involved in Capsular Polysaccharide Biosynthesis.
Authors: Gruszczyk, J. / Fleurie, A. / Olivares-Illana, V. / Bechet, E. / Zanella-Cleon, I. / Morera, S. / Meyer, P. / Pompidor, G. / Kahn, R. / Grangeasse, C. / Nessler, S.
History
DepositionAug 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cap5O
B: Cap5O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,98112
Polymers96,3472
Non-polymers2,63310
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9890 Å2
ΔGint-52 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.220, 131.497, 158.820
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 Cap5O


Mass: 48173.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Reynolds and Newman / Gene: cap5O / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P95708
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID / Dipicolinic acid


Mass: 167.119 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-EU / EUROPIUM ION / Europium


Mass: 151.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Eu
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15mg/ml CAP5O, 5mM NAD, 50mM Eu(PDC)3, 32% PEG 4000, 0.2M sodium acetate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.2525 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2008
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2525 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 30070 / Num. obs: 30070 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 58.07 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.104 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4196 / Rsym value: 0.719 / % possible all: 98.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.63 Å / Cor.coef. Fo:Fc: 0.9275 / Cor.coef. Fo:Fc free: 0.8997 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1525 5.08 %RANDOM
Rwork0.2012 ---
all0.2035 30007 --
obs0.2035 30007 --
Displacement parametersBiso mean: 57.66 Å2
Baniso -1Baniso -2Baniso -3
1--5.2618 Å20 Å20 Å2
2--13.1736 Å20 Å2
3----7.9119 Å2
Refine analyzeLuzzati coordinate error obs: 0.315 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 162 120 6747
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0167512
X-RAY DIFFRACTIONt_angle_deg1.2891742
X-RAY DIFFRACTIONt_dihedral_angle_d23632
X-RAY DIFFRACTIONt_trig_c_planes0.00741942
X-RAY DIFFRACTIONt_gen_planes0.01479405
X-RAY DIFFRACTIONt_it675120
X-RAY DIFFRACTIONt_nbd25
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion19.9
X-RAY DIFFRACTIONt_chiral_improper_torsion8975
X-RAY DIFFRACTIONt_ideal_dist_contact79634
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.269 135 4.86 %
Rwork0.2183 2640 -
all0.2208 2775 -
obs-2775 -

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