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- PDB-1vic: Crystal structure of CMP-KDO synthetase -

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Basic information

Entry
Database: PDB / ID: 1vic
TitleCrystal structure of CMP-KDO synthetase
Components3-deoxy-manno-octulosonate cytidylyltransferase
KeywordsTRANSFERASE / structural genomics
Function / homology
Function and homology information


3-deoxy-manno-octulosonate cytidylyltransferase / 3-deoxy-manno-octulosonate cytidylyltransferase activity / CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / lipopolysaccharide biosynthetic process / cytosol
Similarity search - Function
3-deoxy-D-manno-octulosonate cytidylyltransferase / Acylneuraminate cytidylyltransferase / Cytidylyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-deoxy-manno-octulosonate cytidylyltransferase
B: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)58,5212
Polymers58,5212
Non-polymers00
Water7,873437
1
A: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)29,2601
Polymers29,2601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)29,2601
Polymers29,2601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-18 kcal/mol
Surface area22030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.973, 131.921, 43.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 3-deoxy-manno-octulosonate cytidylyltransferase / CMP-KDO synthetase / CMP-2-keto-3-deoxyoctulosonic acid synthetase / CKS


Mass: 29260.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: KDSB, HI0058 / Production host: Escherichia coli (E. coli)
References: UniProt: P44490, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→38.62 Å / Num. all: 44705 / Num. obs: 44705 / % possible obs: 95.4 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.9 / % possible all: 99.6
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.62 Å / σ(F): 0
RfactorNum. reflection
Rfree0.273 2252
Rwork0.236 -
obs-44705
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 319.47 Å2 / ksol: 0.851 e/Å3
Displacement parametersBiso mean: 26.662 Å2
Baniso -1Baniso -2Baniso -3
1--1.263 Å20 Å20 Å2
2---0.388 Å20 Å2
3---1.651 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.8→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 0 437 4340
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_d1.362
X-RAY DIFFRACTIONp_planar_tor1.241
X-RAY DIFFRACTIONp_chiral_restr0.095
X-RAY DIFFRACTIONp_plane_restr0.007
X-RAY DIFFRACTIONp_mcbond_it2.451
X-RAY DIFFRACTIONp_mcangle_it3.937
X-RAY DIFFRACTIONp_scbond_it4.488
X-RAY DIFFRACTIONp_scangle_it6.613
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4

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