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- PDB-2y6p: Evidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltrans... -

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Basic information

Entry
Database: PDB / ID: 2y6p
TitleEvidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase KdsB
Components3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
KeywordsTRANSFERASE / LIPID A
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
BETA-MERCAPTOETHANOL / CYTIDINE-5'-TRIPHOSPHATE / ISOPROPYL ALCOHOL / 3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.1 Å
AuthorsSchmidt, H. / Mesters, J.R. / Mamat, U. / Hilgenfeld, R.
CitationJournal: Plos One / Year: 2011
Title: Evidence for a Two-Metal-Ion Mechanism in the Cytidyltransferase Kdsb, an Enzyme Involved in Lipopolysaccharide Biosynthesis.
Authors: Schmidt, H. / Mesters, J.R. / Wu, J. / Woodard, R.W. / Hilgenfeld, R. / Mamat, U.
History
DepositionJan 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 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 / struct_site
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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
C: 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,43415
Polymers81,6403
Non-polymers1,79412
Water3,459192
1
A: 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
B: 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,62910
Polymers54,4272
Non-polymers1,2028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-59.8 kcal/mol
Surface area20060 Å2
MethodPISA
2
C: 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
hetero molecules

C: 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,61110
Polymers54,4272
Non-polymers1,1848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5280 Å2
ΔGint-65.1 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.175, 51.175, 107.514
Angle α, β, γ (deg.)90.00, 102.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 27213.490 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Plasmid: PT7-KDSB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 CODONPLUS(DE3) / Variant (production host): PRIL
References: UniProt: O66914, 3-deoxy-manno-octulosonate cytidylyltransferase

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Non-polymers , 5 types, 204 molecules

#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.57 Å3/Da / Density % sol: 46.9 % / Description: NONE
Crystal growpH: 7.5
Details: THE DROPS CONTAINED EQUAL AMOUNTS OF KDSB (10 MG/ML IN 20 MM TRIS-HCL, PH 7.5, 100 MM NACL, 5 MM MGCL2, 2 MM 2-MERCAPTOETHANOL, SUPPLEMENTED WITH 1 MM CTP) AND RESERVOIR SOLUTION (0.1 M ...Details: THE DROPS CONTAINED EQUAL AMOUNTS OF KDSB (10 MG/ML IN 20 MM TRIS-HCL, PH 7.5, 100 MM NACL, 5 MM MGCL2, 2 MM 2-MERCAPTOETHANOL, SUPPLEMENTED WITH 1 MM CTP) AND RESERVOIR SOLUTION (0.1 M HEPES PH 7.5, 18.8% ISOPROPANOL, 18.7% PEG 4000).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.834
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Sep 14, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.834 Å / Relative weight: 1
ReflectionResolution: 2.1→29.36 Å / Num. obs: 46213 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.75 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.74
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 6.12 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.1→29.35 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.128 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25792 2263 5.1 %RANDOM
Rwork0.21129 ---
obs0.21369 42413 91.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.206 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å21.8 Å2
2--0.78 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5673 0 105 192 5970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225878
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3752.0267952
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02423.7273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.106151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4911553
X-RAY DIFFRACTIONr_chiral_restr0.0910.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214318
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5431.53466
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03925649
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.81632412
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.14.52302
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 171 -
Rwork0.241 2983 -
obs--88.6 %
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)
11.05720.432-0.61411.1032-0.46620.83250.179-0.27960.04160.2078-0.1451-0.0677-0.09580.4247-0.03390.0959-0.05220.00710.2449-0.05180.092263.462157.66815.9802
20.63630.4262-0.28360.50240.03551.24860.01010.02580.05780.06980.0370.0730.0967-0.07-0.04710.14990.0310.01010.01950.01360.1332.785633.117416.9918
33.41-0.4033-1.65140.6115-0.34372.90490.01390.09010.1526-0.0130.03290.0443-0.03680.0323-0.04680.0255-0.039-0.00360.2132-0.02840.032546.599153.819652.2822
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 232
2X-RAY DIFFRACTION2B2 - 234
3X-RAY DIFFRACTION3C3 - 231

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