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- PDB-1vh3: Crystal structure of CMP-KDO synthetase -

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Basic information

Entry
Database: PDB / ID: 1vh3
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
Chem-CMK / 3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 2.7 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: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-deoxy-manno-octulosonate cytidylyltransferase
B: 3-deoxy-manno-octulosonate cytidylyltransferase
C: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5715
Polymers88,4853
Non-polymers1,0872
Water1,69394
1
A: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0382
Polymers29,4951
Non-polymers5431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0382
Polymers29,4951
Non-polymers5431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)29,4951
Polymers29,4951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.480, 48.281, 96.488
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: 29494.869 Da / Num. of mol.: 3
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: Chemical ChemComp-CMK / CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID / CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID


Mass: 543.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H26N3O15P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.35 %
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, 0.9641
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.96411
ReflectionResolution: 2.7→19.96 Å / Num. all: 22726 / Num. obs: 22726 / % possible obs: 96 % / Redundancy: 3.58 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.5
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 5.9 / % possible all: 91.8
Reflection
*PLUS
Redundancy: 3.6 %
Reflection shell
*PLUS
% possible obs: 91.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC4refinement
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 2.7→19.95 Å / σ(F): 0
RfactorNum. reflection
Rfree0.307 1162
Rwork0.256 -
obs-22724
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 58.157 Å2 / ksol: 0.838 e/Å3
Displacement parametersBiso mean: 49.654 Å2
Baniso -1Baniso -2Baniso -3
1--1.062 Å20 Å20 Å2
2--0.583 Å20 Å2
3---0.48 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.7→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 108 94 5485
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.031
X-RAY DIFFRACTIONp_angle_d2.337
X-RAY DIFFRACTIONp_planar_tor3.388
X-RAY DIFFRACTIONp_chiral_restr0.135
X-RAY DIFFRACTIONp_plane_restr0.044
X-RAY DIFFRACTIONp_mcbond_it1.252
X-RAY DIFFRACTIONp_mcangle_it2.311
X-RAY DIFFRACTIONp_scbond_it1.912
X-RAY DIFFRACTIONp_scangle_it2.971
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.3

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