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- PDB-3tqd: Structure of the 3-deoxy-D-manno-octulosonate cytidylyltransferas... -

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Basic information

Entry
Database: PDB / ID: 3tqd
TitleStructure of the 3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) from Coxiella burnetii
Components3-deoxy-manno-octulosonate cytidylyltransferase
KeywordsTRANSFERASE / Cell envelope
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
ACETATE ION / NICKEL (II) ION / 3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFranklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2073
Polymers29,0891
Non-polymers1182
Water3,063170
1
A: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)58,4146
Polymers58,1782
Non-polymers2354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2860 Å2
ΔGint-38 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.752, 51.616, 78.874
Angle α, β, γ (deg.)90.00, 111.92, 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: 29089.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_0479, kdsB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83E52, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES -3 TO 0 REPRESENT AN INCORRECTLY CHOSEN N TERMINUS FOR THIS EXPRESSION CONSTRUCT

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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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M ammonium acetate, 0.085 M Na citrate, 25.5% PEG 4000, 15% glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 15, 2011
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 23582 / Num. obs: 23093 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rsym value: 0.053 / Net I/σ(I): 39.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1186 / Rsym value: 0.454 / % possible all: 88

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3K8D

3k8d


Resolution: 1.8→25.62 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.379 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22746 1184 5.2 %RANDOM
Rwork0.1882 ---
obs0.19026 22946 96.97 %-
all-23663 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.27 Å2
2--2.06 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 5 170 2096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221966
X-RAY DIFFRACTIONr_bond_other_d0.0010.021330
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9592666
X-RAY DIFFRACTIONr_angle_other_deg0.97633231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05223.91897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42815325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8241515
X-RAY DIFFRACTIONr_chiral_restr0.1010.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212199
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
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_it1.0181.51215
X-RAY DIFFRACTIONr_mcbond_other0.3011.5486
X-RAY DIFFRACTIONr_mcangle_it1.74721957
X-RAY DIFFRACTIONr_scbond_it2.7813751
X-RAY DIFFRACTIONr_scangle_it4.4184.5709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 72 -
Rwork0.306 1409 -
obs--84.29 %
Refinement TLS params.Method: refined / Origin x: -5.344 Å / Origin y: 42.4897 Å / Origin z: 17.326 Å
111213212223313233
T0.0735 Å2-0.0183 Å2-0.0282 Å2-0.0639 Å2-0.0114 Å2--0.1059 Å2
L1.4572 °2-0.0438 °2-1.3794 °2-0.6737 °2-0.3053 °2--5.1591 °2
S0.0082 Å °-0.2806 Å °-0.0023 Å °0.1488 Å °-0.0025 Å °-0.0387 Å °0.0588 Å °0.1693 Å °-0.0057 Å °

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