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- PDB-3jtj: 3-deoxy-manno-octulosonate cytidylyltransferase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3jtj
Title3-deoxy-manno-octulosonate cytidylyltransferase from Yersinia pestis
Components3-deoxy-manno-octulosonate cytidylyltransferase
KeywordsTRANSFERASE / structural genomics / IDP02355 / 3-deoxy-manno-octulosonate cytidylyltransferase / Lipopolysaccharide biosynthesis / Nucleotidyltransferase / Center for Structural Genomics of Infectious Diseases / CSGID
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
IMIDAZOLE / 3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.18 Å
AuthorsOsipiuk, J. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Yersinia pestis.
Authors: Osipiuk, J. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0583
Polymers27,9201
Non-polymers1382
Water2,018112
1
A: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules

A: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1166
Polymers55,8402
Non-polymers2764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3220 Å2
ΔGint-9 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.058, 97.058, 93.626
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 27919.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: kdsB, y2772, YPO1400, YP_1193 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZGA4, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.56 Å3/Da / Density % sol: 73.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M calcium chloride, 20% PEG-3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.18→43.1 Å / Num. all: 26852 / Num. obs: 26852 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.8 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.107 / Χ2: 3.044 / Net I/σ(I): 10.3
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 2.97 / Num. unique all: 1310 / Χ2: 1.101 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.18→43.2 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 8.18 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1346 5 %RANDOM
Rwork0.182 ---
all0.183 26816 --
obs0.183 26816 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.75 Å2 / Biso mean: 39.689 Å2 / Biso min: 21.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20.8 Å20 Å2
2--1.61 Å20 Å2
3----2.41 Å2
Refinement stepCycle: LAST / Resolution: 2.18→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 10 112 2038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221978
X-RAY DIFFRACTIONr_bond_other_d0.0020.021322
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9582693
X-RAY DIFFRACTIONr_angle_other_deg0.95233213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3325252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52823.48389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50215317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9011517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212233
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
X-RAY DIFFRACTIONr_mcbond_it0.9651.51249
X-RAY DIFFRACTIONr_mcbond_other0.2371.5501
X-RAY DIFFRACTIONr_mcangle_it1.87322015
X-RAY DIFFRACTIONr_scbond_it3.1183729
X-RAY DIFFRACTIONr_scangle_it5.1334.5676
LS refinement shellResolution: 2.181→2.238 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 80 -
Rwork0.243 1723 -
all-1803 -
obs-1803 91.85 %
Refinement TLS params.Method: refined / Origin x: 45.6947 Å / Origin y: 39.9149 Å / Origin z: 0.5274 Å
111213212223313233
T0.0887 Å20.0276 Å20.0151 Å2-0.1841 Å20.0075 Å2--0.0226 Å2
L1.2052 °2-0.5659 °20.584 °2-1.1317 °2-0.3284 °2--0.7538 °2
S0.054 Å °0.0338 Å °0.0887 Å °-0.006 Å °-0.1125 Å °-0.1021 Å °0.0054 Å °0.1602 Å °0.0585 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 250
2X-RAY DIFFRACTION1A301 - 302
3X-RAY DIFFRACTION1A251 - 364

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