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- PDB-3k8d: Crystal structure of E. coli lipopolysaccharide specific CMP-KDO ... -

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Basic information

Entry
Database: PDB / ID: 3k8d
TitleCrystal structure of E. coli lipopolysaccharide specific CMP-KDO synthetase in complex with CTP and 2-deoxy-Kdo
Components3-deoxy-manno-octulosonate cytidylyltransferase
KeywordsTRANSFERASE / KdsB synthetase KDO complex / Lipopolysaccharide biosynthesis / Magnesium / Nucleotidyltransferase
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 / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / magnesium ion binding / 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-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHeyes, D.J. / Levy, C.W. / Lafite, P. / Scrutton, N.S. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure-based mechanism of CMP-2-keto-3-deoxymanno-octulonic acid synthetase: convergent evolution of a sugar-activating enzyme with DNA/RNA polymerases
Authors: Heyes, D.J. / Levy, C. / Lafite, P. / Roberts, I.S. / Goldrick, M. / Stachulski, A.V. / Rossington, S.B. / Stanford, D. / Rigby, S.E.J. / Scrutton, N.S. / Leys, D.
History
DepositionOct 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 5, 2012Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
C: 3-deoxy-manno-octulosonate cytidylyltransferase
D: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,80816
Polymers117,8264
Non-polymers2,98312
Water22,6091255
1
A: 3-deoxy-manno-octulosonate cytidylyltransferase
D: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4048
Polymers58,9132
Non-polymers1,4916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-35 kcal/mol
Surface area18760 Å2
MethodPISA
2
B: 3-deoxy-manno-octulosonate cytidylyltransferase
C: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4048
Polymers58,9132
Non-polymers1,4916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-36 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.770, 94.770, 153.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
3-deoxy-manno-octulosonate cytidylyltransferase / CMP-KDO synthetase / CMP-2-keto-3-deoxyoctulosonic acid synthetase / CKS


Mass: 29456.377 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12
References: UniProt: P04951, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Sugar
ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H14O8
IdentifierTypeProgram
DKdopaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-KdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdoSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 1255 / Source method: isolated from a natural source / Formula: H2O

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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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5mM CTP, 5mM 2-deoxy Kdo, 85mM HEPES, pH7.5, 17% PEG10000, 6.8% ethylene glycol, 15% (v/v), VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.898→45.3 Å / Num. obs: 121076 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.3 / % possible all: 99.1

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Processing

Software
NameClassification
DNAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VH1

1vh1


Resolution: 1.9→45.27 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.182 6127 5.06 %Random
Rwork0.151 ---
obs0.153 121076 99.6 %-
all-121076 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.84 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7630 0 180 1255 9065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078087
X-RAY DIFFRACTIONf_angle_d1.14211057
X-RAY DIFFRACTIONf_dihedral_angle_d19.8233047
X-RAY DIFFRACTIONf_chiral_restr0.0821238
X-RAY DIFFRACTIONf_plane_restr0.0051440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8983-1.91990.24052030.18483656X-RAY DIFFRACTION95
1.9199-1.94250.22892130.18683789X-RAY DIFFRACTION100
1.9425-1.96620.20141860.1773846X-RAY DIFFRACTION100
1.9662-1.9910.24451900.17553856X-RAY DIFFRACTION100
1.991-2.01720.21981910.16643855X-RAY DIFFRACTION100
2.0172-2.04490.21862110.1663848X-RAY DIFFRACTION100
2.0449-2.07410.20752240.15873809X-RAY DIFFRACTION100
2.0741-2.10510.20742140.16113858X-RAY DIFFRACTION100
2.1051-2.13790.20661680.16243840X-RAY DIFFRACTION100
2.1379-2.1730.2211950.16383840X-RAY DIFFRACTION100
2.173-2.21050.20921910.16293860X-RAY DIFFRACTION100
2.2105-2.25070.19251970.16083889X-RAY DIFFRACTION100
2.2507-2.29390.19761940.15423800X-RAY DIFFRACTION100
2.2939-2.34080.21780.15633924X-RAY DIFFRACTION100
2.3408-2.39170.20372150.16443796X-RAY DIFFRACTION100
2.3917-2.44730.19851930.15273874X-RAY DIFFRACTION100
2.4473-2.50850.181950.15323849X-RAY DIFFRACTION100
2.5085-2.57630.20851920.15383832X-RAY DIFFRACTION100
2.5763-2.65210.19432250.15583832X-RAY DIFFRACTION100
2.6521-2.73770.20862290.15733811X-RAY DIFFRACTION100
2.7377-2.83550.17532130.153797X-RAY DIFFRACTION100
2.8355-2.9490.17242400.14923842X-RAY DIFFRACTION100
2.949-3.08320.18221950.163822X-RAY DIFFRACTION100
3.0832-3.24570.18212230.15383836X-RAY DIFFRACTION100
3.2457-3.4490.15452090.13983842X-RAY DIFFRACTION100
3.449-3.71520.15232130.12753812X-RAY DIFFRACTION100
3.7152-4.08890.15361960.1323887X-RAY DIFFRACTION100
4.0889-4.680.12762210.11423810X-RAY DIFFRACTION100
4.68-5.89430.14932180.13073832X-RAY DIFFRACTION100
5.8943-45.28040.191950.16613805X-RAY DIFFRACTION99

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