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- PDB-1gqc: THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE... -

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Basic information

Entry
Database: PDB / ID: 1gqc
TitleTHE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE COMPLEXED WITH CMP-Kdo at 100K
Components3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE / 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'-MONOPHOSPHATE / Chem-CMK / 3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.6 Å
AuthorsJelakovic, S. / Schulz, G.E.
Citation
Journal: Biochemistry / Year: 2002
Title: Catalytic Mechanism of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase as Derived from Complexes with Reaction Educt and Product.
Authors: Jelakovic, S. / Schulz, G.E.
#1: 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.
#2: 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
DepositionNov 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2002Provider: 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)55,0356
Polymers54,1202
Non-polymers9154
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.944, 130.996, 48.148
Angle α, β, γ (deg.)90.00, 102.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.081444, 0.885712, -0.457036), (0.836788, -0.188342, -0.514113), (-0.541435, -0.424314, -0.725814)
Vector: 0.027, 89.549, 153.567)

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Components

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


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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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.: 1 / Source method: obtained synthetically / Formula: C17H26N3O15P
#4: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growpH: 9.4 / Details: pH 9.40
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Jelakovic, S., (2001) J.Mol.Biol., 312, 143.
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: 100 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: 2.6→33 Å / Num. obs: 15622 / % possible obs: 88 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 6
Reflection
*PLUS
Lowest resolution: 33 Å / % possible obs: 88 %
Reflection shell
*PLUS
Highest resolution: 2.57 Å / Lowest resolution: 2.7 Å / % possible obs: 81 % / Redundancy: 5.7 % / Num. unique obs: 2075 / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.6→24.44 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 -4.9 %RANDOM
Rwork0.178 ---
obs0.178 15151 88.4 %-
Refinement stepCycle: LAST / Resolution: 2.6→24.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 59 267 4069
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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