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- PDB-3k8e: Crystal structure of E. coli lipopolysaccharide specific CMP-KDO ... -

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Basic information

Entry
Database: PDB / ID: 3k8e
TitleCrystal structure of E. coli lipopolysaccharide specific CMP-KDO synthetase
Components3-deoxy-manno-octulosonate cytidylyltransferase
KeywordsTRANSFERASE / KdsB synthetase deoxy 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
3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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: Advisory / Version format compliance
Revision 1.2Dec 5, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 3-deoxy-manno-octulosonate cytidylyltransferase
D: 3-deoxy-manno-octulosonate cytidylyltransferase
A: 3-deoxy-manno-octulosonate cytidylyltransferase
B: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)117,8264
Polymers117,8264
Non-polymers00
Water2,558142
1
C: 3-deoxy-manno-octulosonate cytidylyltransferase
D: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)58,9132
Polymers58,9132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-18 kcal/mol
Surface area20930 Å2
MethodPISA
2
A: 3-deoxy-manno-octulosonate cytidylyltransferase
B: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)58,9132
Polymers58,9132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-17 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.470, 77.180, 143.630
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100mM sodium acetate, pH4.6, 250mM sodium sulfate, 15% glycerol, 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: 2.5→47 Å / Num. all: 46074 / Num. obs: 46074 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2.51→2.57 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 4.97 / % possible all: 97

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VH1

1vh1


Resolution: 2.51→47 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 17.399 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23397 2360 5.1 %RANDOM
Rwork0.19871 ---
obs0.20055 43817 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.485 Å2
Baniso -1Baniso -2Baniso -3
1-4.64 Å20 Å2-0.02 Å2
2--0.65 Å20 Å2
3----5.29 Å2
Refinement stepCycle: LAST / Resolution: 2.51→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7515 0 0 142 7657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227663
X-RAY DIFFRACTIONr_bond_other_d0.0010.025129
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.94810427
X-RAY DIFFRACTIONr_angle_other_deg0.933312417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78723.288371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.892151217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.591577
X-RAY DIFFRACTIONr_chiral_restr0.0770.21179
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028661
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021584
X-RAY DIFFRACTIONr_nbd_refined0.2180.21571
X-RAY DIFFRACTIONr_nbd_other0.1970.25189
X-RAY DIFFRACTIONr_nbtor_refined0.180.23710
X-RAY DIFFRACTIONr_nbtor_other0.0860.24150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2185
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5281.54963
X-RAY DIFFRACTIONr_mcbond_other0.0971.51950
X-RAY DIFFRACTIONr_mcangle_it0.87227766
X-RAY DIFFRACTIONr_scbond_it1.41233048
X-RAY DIFFRACTIONr_scangle_it2.24.52661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.505→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 164 -
Rwork0.275 3132 -
obs--95.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.75470.3591-1.53912.45331.48964.67670.0586-0.27560.642-0.3112-0.02930.2542-0.34080.0765-0.0293-0.1048-0.0468-0.057-0.0081-0.0326-0.164222.6942-54.865384.3687
24.969-0.5641.63143.741-0.48756.28240.02-0.2190.05180.0857-0.08670.1698-0.32650.04630.0668-0.1224-0.03250.0301-0.2068-0.0716-0.227918.4616-60.823163.5821
36.1466-3.3189-5.52419.77496.98647.0053-0.06550.3694-0.0145-0.4590.07650.37280.1431-0.3365-0.011-0.1927-0.093-0.0190.15570.00690.02345.5727-59.385583.518
42.9999-0.2371.65934.753-0.20078.25750.03460.1287-0.0222-0.12120.04280.6086-0.5621-0.058-0.0774-0.1386-0.04930.0394-0.15920.049-0.188519.8344-68.83426.0744
52.8135-0.9369-1.37155.49871.35454.65270.04990.2290.0807-0.3466-0.10120.3264-0.71080.02130.0514-0.0603-0.0722-0.0777-0.18880.0058-0.222518.131-61.493146.9015
60.76070.76062.51414.92363.78248.6958-0.617-0.98330.68530.03420.26111.5369-1.3374-0.63260.35580.54270.3724-0.13920.22520.07690.55497.2756-56.1526.3474
73.6414-0.0647-2.2424.7719-0.20748.3383-0.0073-0.0797-0.05290.12650.03960.56350.6098-0.0846-0.0322-0.10670.0536-0.0448-0.15630.0423-0.208219.9908-21.322445.7862
82.53310.88941.36765.46441.09114.95020.0414-0.1759-0.07720.3034-0.12990.33430.71850.03020.0886-0.08460.07310.0832-0.18240.006-0.211717.8702-28.833724.7756
90.27241.73610.716511.16494.16063.4939-0.54750.97440.2403-0.65290.53221.88091.2367-0.46090.01520.5091-0.30840.0640.31620.10870.48586.9458-33.387144.8124
106.18-0.3761.6492.85391.23564.25950.05490.2869-0.58320.1812-0.04110.25290.25920.0245-0.0138-0.10930.05580.0597-0.0186-0.0093-0.203822.4835-34.5411-12.9001
114.02930.3306-0.99223.90950.11015.9659-0.00020.1928-0.0735-0.0922-0.02270.11230.2930.14330.0229-0.12940.0326-0.0182-0.1972-0.0559-0.232718.8344-29.42587.9413
126.95242.67465.08927.50831.51995.7857-0.1297-0.60710.1109-0.2479-0.1250.1361-0.3565-0.6840.2547-0.20410.11940.01670.1955-0.00370.04635.7111-30.4095-12.0487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 117
2X-RAY DIFFRACTION2A118 - 227
3X-RAY DIFFRACTION3A228 - 246
4X-RAY DIFFRACTION4B3 - 117
5X-RAY DIFFRACTION5B118 - 227
6X-RAY DIFFRACTION6B228 - 247
7X-RAY DIFFRACTION7C3 - 117
8X-RAY DIFFRACTION8C118 - 227
9X-RAY DIFFRACTION9C228 - 245
10X-RAY DIFFRACTION10D3 - 117
11X-RAY DIFFRACTION11D118 - 227
12X-RAY DIFFRACTION12D228 - 247

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