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- PDB-1h6j: The three-dimensional structure of capsule-specific CMP:2-keto-3-... -

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Basic information

Entry
Database: PDB / ID: 1h6j
TitleThe three-dimensional structure of capsule-specific CMP:2-keto-3-deoxy-manno-octonic acid synthetase from Escherichia coli
Components3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
KeywordsNUCLEOTIDYLTRANSFERASE / CMP-KDO SYNTHETASE / CAPSULAR POLYSACCHARIDE / SACCHARIDE ACTIVATION
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 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.32 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B
AuthorsJelakovic, S. / Jann, K. / Schulz, G.E.
CitationJournal: 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
DepositionJun 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: 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)54,1202
Polymers54,1202
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.090, 133.460, 48.330
Angle α, β, γ (deg.)90.00, 102.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.044215, 0.857698, -0.51225), (0.857496, -0.230505, -0.459966), (-0.512587, -0.459589, -0.725281)
Vector: 2.307, 89.301, 153.674)

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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 / Coordinate model: Cα atoms only


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.13 %
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
116 %PEG200001drop
2100 mMTris-HCl1drop
3200 mMcadmium acetate1drop
45 mM1dropMgCl2
52 mMdithiothreitol1drop
62-4 %PEG200001reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 22560 / % possible obs: 95 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 95 %

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.32→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1091 5 %RANDOM
Rwork0.225 ---
obs0.225 21233 90 %-
Refinement stepCycle: LAST / Resolution: 2.32→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms482 0 0 0 482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
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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