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- PDB-4phr: Domain of unknown function 1792 (DUF1792) with manganese -

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Basic information

Entry
Database: PDB / ID: 4phr
TitleDomain of unknown function 1792 (DUF1792) with manganese
ComponentsPutative glycosyltransferase (GalT1)
KeywordsTRANSFERASE / Domain of unknown function 1792 (DUF1792) / Glycosyltransferase
Function / homologyGlycosyltransferase 2-like / Glycosyltransferase GT-D fold / Nucleotide-diphospho-sugar transferases / Glycosyl transferase family 2 / Glycosyltransferase GT-D fold / transferase activity / nucleotide binding / Putative glycosyltransferase (GalT1)
Function and homology information
Specimen sourceStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsZhang, H. / Wu, H.
CitationJournal: Nat Commun / Year: 2014
Title: The highly conserved domain of unknown function 1792 has a distinct glycosyltransferase fold.
Authors: Zhang, H. / Zhu, F. / Yang, T. / Ding, L. / Zhou, M. / Li, J. / Haslam, S.M. / Dell, A. / Erlandsen, H. / Wu, H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 6, 2014 / Release: Aug 6, 2014
RevisionDateData content typeGroupProviderType
1.0Aug 6, 2014Structure modelrepositoryInitial release
1.1Feb 4, 2015Structure modelDerived calculations
1.2Oct 14, 2015Structure modelData collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative glycosyltransferase (GalT1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7235
Polymers32,1461
Non-polymers5774
Water4,792266
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)71.474, 45.409, 78.782
Angle α, β, γ (deg.)90.00, 109.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-502-

HOH

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Components

#1: Protein/peptide Putative glycosyltransferase (GalT1)


Mass: 32145.566 Da / Num. of mol.: 1 / Fragment: UNP residues 1-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus parasanguinis (bacteria) / Strain: FW213 / Gene: galT1, Spaf_1933 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: I1ZPA1
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Uridine diphosphate / Comment: UDP *YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Manganese
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Acetate
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 1.87 Å3/Da / Density % sol: 34.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris buffer, PEG 1500, NaAcetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 52820 / % possible obs: 98.6 % / Redundancy: 5.5 % / Net I/σ(I): 52.6

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→37.64 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 2697 5.11 %
Rwork0.147 --
Obs0.149 52818 98.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.5 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.581 Å20 Å2-0.6578 Å2
2---0.1003 Å20 Å2
3----0.4807 Å2
Refinement stepCycle: LAST / Resolution: 1.34→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 34 266 2564
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0052342
f_angle_d1.1533164
f_dihedral_angle_d14.222875
f_chiral_restr0.077341
f_plane_restr0.005401
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3399-1.36420.25871290.1982230186
1.3642-1.39050.24091540.1698257299
1.3905-1.41880.24131670.1509266699
1.4188-1.44970.21751520.1464259399
1.4497-1.48340.22231310.1355265999
1.4834-1.52050.18761300.1324265899
1.5205-1.56160.2021350.1249268799
1.5616-1.60760.18121560.1174257699
1.6076-1.65950.18921360.1245263899
1.6595-1.71880.21721300.1341265199
1.7188-1.78760.20541410.1317262799
1.7876-1.8690.18441400.1311263799
1.869-1.96750.17651530.1345265399
1.9675-2.09070.18881370.13872659100
2.0907-2.25220.16571490.13642675100
2.2522-2.47880.18621450.14182697100
2.4788-2.83730.19781420.15682695100
2.8373-3.57430.17061220.15462729100
3.5743-37.65220.18471480.1629274899

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