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- PDB-4r16: Structure of UDP-D-MAnNAc dehdrogeanse from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 4r16
TitleStructure of UDP-D-MAnNAc dehdrogeanse from Pyrococcus horikoshii
Components418aa long hypothetical UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


UDP-N-acetyl-D-mannosamine dehydrogenase / UDP-N-acetyl-D-mannosamine dehydrogenase activity / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / polysaccharide biosynthetic process / 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
Chem-SAJ / UDP-N-acetyl-D-mannosamine dehydrogenase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsPampa, K.J. / Lokanath, N.K. / Rai, R.V. / Kunishima, N.
CitationJournal: To be Published
Title: Structure of UDP-D-MAnNAc dehdrogeanse from Pyrococcus horikoshii
Authors: Pampa, K.J. / Lokanath, N.K. / Rai, R.V. / Kunishima, N.
History
DepositionAug 4, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 418aa long hypothetical UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase
B: 418aa long hypothetical UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4824
Polymers93,2392
Non-polymers1,2432
Water18,2311012
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-50 kcal/mol
Surface area32340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.030, 74.650, 73.560
Angle α, β, γ (deg.)66.20, 70.40, 75.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 418aa long hypothetical UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase / UDP-D-MAnNAc dehdrogeanse


Mass: 46619.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: PH1618 / Production host: Escherichia coli (E. coli) / References: UniProt: O59284
#2: Chemical ChemComp-SAJ / (2S,3S,4R,5S,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,4-bis(oxidanyl)oxane-2-carboxylic acid


Mass: 621.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25N3O18P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1012 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: PEG 8000, 0.1M HEPES, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9311, 0.9721, 0.9521
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 9, 2014
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93111
20.97211
30.95211
ReflectionResolution: 1.55→50 Å / Num. all: 136913 / Num. obs: 135913 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.55→1.61 Å / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.55→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 6902 4.8 %Random
Rwork0.2243 129009 --
all-136913 --
obs-135911 95.4 %-
Solvent computationBsol: 39.2902 Å2
Displacement parametersBiso max: 55.3 Å2 / Biso mean: 23.2663 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--4.259 Å2-1.018 Å21.548 Å2
2---0.559 Å21.528 Å2
3---4.818 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6498 0 80 1012 7590
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1731.5
X-RAY DIFFRACTIONc_scbond_it2.1262
X-RAY DIFFRACTIONc_mcangle_it1.6852
X-RAY DIFFRACTIONc_scangle_it2.842.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3sag.par

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