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- PDB-1h7g: The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase... -

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Basic information

Entry
Database: PDB / ID: 1h7g
TitleThe structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogues, CTP MG2+ complex
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
CYTIDINE-5'-TRIPHOSPHATE / 3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.13 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6274
Polymers54,1202
Non-polymers5072
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.040, 133.580, 48.410
Angle α, β, γ (deg.)90.00, 102.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.051044, 0.856058, -0.514353), (0.855212, -0.228508, -0.465185), (-0.515759, -0.463625, -0.720447)
Vector: 2.798, 89.693, 153.952)

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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 / Gene: KPSU / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P42216, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
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: 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: 2.13→23.7 Å / Num. obs: 26977 / % possible obs: 85 % / Redundancy: 1.8 % / Rsym value: 0.058
Reflection
*PLUS
% possible obs: 85 % / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Highest resolution: 2.13 Å / Lowest resolution: 2.2 Å / % possible obs: 71 % / Redundancy: 1.5 % / Num. unique obs: 2184 / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5

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Processing

SoftwareName: X-PLOR / Version: 3.851 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.13→24 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 -3.2 %RANDOM
Rwork0.175 ---
obs0.175 25997 82 %-
Refinement stepCycle: LAST / Resolution: 2.13→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 30 423 4219
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.3
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
Software
*PLUS
Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 24 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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