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- PDB-1h7e: The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase... -

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Basic information

Entry
Database: PDB / ID: 1h7e
TitleThe structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogues, Apo-enzyme
Components3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
KeywordsNUCLEOTIDYLTRANSFERASE / CMP-KDO SYNTHETASE / NUCLEOSIDE MONOPHOSPHATE GLYCOSIDES / LIPOPOLYSACCHARIDE BIOSYNTHESIS / SUGAR-ACTIVATING ENZYMES
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 speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.83 Å
AuthorsJelakovic, S. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase and of its Complexes with Substrates and Substrate Analogs
Authors: Jelakovic, S. / Schulz, G.E.
#1: Journal: FEBS Lett. / Year: 1996
Title: The Three-Dimensional Structure of Capsule-Specific Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase from Escherichia Coli
Authors: Jelakovic, S. / Jann, K. / Schulz, G.E.
History
DepositionJul 6, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)54,1202
Polymers54,1202
Non-polymers00
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.100, 133.800, 48.480
Angle α, β, γ (deg.)90.00, 102.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.047212, 0.85609, -0.514665), (0.855935, -0.230933, -0.46265), (-0.514923, -0.462363, -0.721855)
Vector: 2.615, 89.725, 153.976)

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Components

#1: Protein 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE / CMP-KDO SYNTHETASE / CKS / CMP-2-KETO-3-DEOXYOCTULOSONIC ACID SYNTHETASE / CMP-2-KETO-3-DEOXY-MANNO ...CMP-KDO SYNTHETASE / CKS / CMP-2-KETO-3-DEOXYOCTULOSONIC ACID SYNTHETASE / CMP-2-KETO-3-DEOXY-MANNO -OCTONIC ACID SYNTHETASE


Mass: 27059.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K5 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P42216, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growpH: 9.4 / Details: pH 9.40
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
28 %(w/v)PEG200001drop
350 mMTris-HCl1drop
4100 mMcalcium acetate1drop
52.5 mM1dropMgCl2
61 mMdithiothreitol1drop
72-4 %PEG200001reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.06
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.83→19.3 Å / Num. obs: 45498 / % possible obs: 90 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.071
Reflection
*PLUS
% possible obs: 90 %
Reflection shell
*PLUS
Highest resolution: 1.83 Å / Lowest resolution: 1.86 Å / % possible obs: 72 % / Redundancy: 3 % / Num. unique obs: 1909 / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6

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Processing

SoftwareName: X-PLOR / Version: 3.851 / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 1.83→19 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.209 -3.1 %RANDOM
Rwork0.161 ---
obs0.161 45498 90 %-
Refinement stepCycle: LAST / Resolution: 1.83→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 0 464 4230
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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