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- PDB-3pol: 2.3 Angstrom Crystal Structure of 3-deoxy-manno-octulosonate Cyti... -

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Basic information

Entry
Database: PDB / ID: 3pol
Title2.3 Angstrom Crystal Structure of 3-deoxy-manno-octulosonate Cytidylyltransferase (kdsB) from Acinetobacter baumannii.
Components3-deoxy-manno-octulosonate cytidylyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha and beta proteins (a/b) / Nucleotide-diphospho-sugar transferases / Cytidylytransferase
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 / cytoplasm
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 speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.3 Angstrom Crystal Structure of 3-deoxy-manno-octulosonate Cytidylyltransferase (kdsB) from Acinetobacter baumannii.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,2061
Polymers31,2061
Non-polymers00
Water1,49583
1
A: 3-deoxy-manno-octulosonate cytidylyltransferase

A: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)62,4132
Polymers62,4132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3040 Å2
ΔGint-14 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.702, 40.832, 56.491
Angle α, β, γ (deg.)90.00, 97.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31206.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 17978 / Gene: A1S_1557, kdsB / Plasmid: pCR2.1-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS
References: UniProt: A3M4Z0, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 7mg/mL, 0.1M Sodium cloride, Tris-HCl (pH 8.3); Screen: Classics II (D7), 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 11015 / Num. obs: 11015 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4 / Num. unique all: 548 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VH1

1vh1


Resolution: 2.3→28.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 15.254 / SU ML: 0.167 / Isotropic thermal model: Individually refined / Cross valid method: THROUGHOUT / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22275 1073 9.8 %RANDOM
Rwork0.17586 ---
all0.18052 9822 --
obs0.18052 9822 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.236 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å22.73 Å2
2---1.44 Å20 Å2
3---2.54 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 0 83 2149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222113
X-RAY DIFFRACTIONr_bond_other_d0.0010.021436
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9772867
X-RAY DIFFRACTIONr_angle_other_deg0.84333513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0175262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77524.563103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.3615376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6251517
X-RAY DIFFRACTIONr_chiral_restr0.0790.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212353
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_mcbond_it1.2661.51318
X-RAY DIFFRACTIONr_mcbond_other0.3391.5523
X-RAY DIFFRACTIONr_mcangle_it2.23122137
X-RAY DIFFRACTIONr_scbond_it3.6523795
X-RAY DIFFRACTIONr_scangle_it5.8634.5730
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 82 -
Rwork0.208 707 -
obs-707 99.37 %
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)
12.0485-2.1894-0.42775.46050.91911.4715-0.04890.0765-0.15950.22850.0068-0.0416-0.0248-0.01250.04220.066-0.0267-0.01740.0107-0.0040.024727.489327.318116.5595
21.7237-1.1422-0.90641.76510.09482.9602-0.1157-0.1192-0.07550.3560.1139-0.0668-0.08180.19870.00170.09620.0009-0.03670.01630.00180.029832.479325.547318.8187
32.94690.3564-0.80193.7107-1.00493.1250.10190.16890.3385-0.2137-0.05560.1664-0.26570.1201-0.04630.04130.02-0.0110.18480.00880.041445.624536.4604-2.7377
41.81721.0721-1.0961.64350.12931.44970.0472-0.3014-0.0670.1265-0.1259-0.0788-0.0530.31840.07870.0442-0.0201-0.02930.1140.02720.012546.710527.490410.1296
55.44851.66055.13915.29-0.50616.22720.12720.3753-0.05590.1356-0.1716-0.13560.12970.18250.04440.1063-0.013-0.03140.1384-0.01030.063520.552141.497110.1471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 43
2X-RAY DIFFRACTION2A44 - 114
3X-RAY DIFFRACTION3A115 - 182
4X-RAY DIFFRACTION4A183 - 233
5X-RAY DIFFRACTION5A234 - 253

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