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- PDB-2c83: CRYSTAL STRUCTURE OF THE SIALYLTRANSFERASE PM0188 -

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Basic information

Entry
Database: PDB / ID: 2c83
TitleCRYSTAL STRUCTURE OF THE SIALYLTRANSFERASE PM0188
ComponentsHYPOTHETICAL PROTEIN PM0188
KeywordsTRANSFERASE / HYPOTHETICAL PROTEIN / PM0188 / SIALYLTRANSFERASE
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
Sialyltransferase, C-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-2,3/2,6-sialyltransferase/sialidase / Sialyltransferase
Similarity search - Component
Biological speciesPASTEURELLA MULTOCIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKim, D.U. / Cho, H.S.
Citation
Journal: Bmb Rep / Year: 2008
Title: Structural analysis of sialyltransferase PM0188 from Pasteurella multocida complexed with donor analogue and acceptor sugar.
Authors: Kim, D.U. / Yoo, J.H. / Lee, Y.J. / Kim, K.S. / Cho, H.S.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural Analysis of the Sialyltransferase Cstii from Campylobacter Jejuni in Complex with a Substrate Analog
Authors: Chiu, C.P. / Watts, A.G. / Lairson, L.L. / Gilbert, M. / Lim, D. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.
#2: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of the Alpha-2,6-Sialyltransferase Pm0188 from Pasteurella Multosida.
Authors: Kim, D.U. / Yoo, J.H. / Ryu, K. / Cho, H.S.
History
DepositionDec 1, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN PM0188


Theoretical massNumber of molelcules
Total (without water)45,6901
Polymers45,6901
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.930, 60.984, 64.635
Angle α, β, γ (deg.)90.00, 112.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HYPOTHETICAL PROTEIN PM0188 / ALPHA-2 / 6-SIALYLTRANSFERASE PM0188


Mass: 45689.582 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PASTEURELLA MULTOCIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CP67, UniProt: Q15KI8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.1 Å3/Da / Density % sol: 40.8 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.9713700, 0.9790300
DetectorType: BRUCKER / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971371
20.979031
ReflectionResolution: 1.9→30 Å / Num. obs: 30006 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 2.1 / % possible all: 93.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→15 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1191 4 %RANDOM
Rwork0.215 ---
obs0.215 24729 82.2 %-
Solvent computationBsol: 41.8875 Å2 / ksol: 0.356479 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-5.076 Å2
2---2.377 Å20 Å2
3---3.097 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 0 132 3338
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018101
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_deg1.96229
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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