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- PDB-3ckv: Crystal Structure of a Mycobacterial Protein -

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Basic information

Entry
Database: PDB / ID: 3ckv
TitleCrystal Structure of a Mycobacterial Protein
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / mycobacteria
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / glycosyltransferase activity / metal ion binding
Similarity search - Function
Glycosyltransferase 2-like / Glycosyl transferase family 2 / 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
URIDINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement / Resolution: 2 Å
AuthorsMarland, Z. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of a UDP-glucose-specific glycosyltransferase from a Mycobacterium species.
Authors: Fulton, Z. / McAlister, A. / Wilce, M.C. / Brammananth, R. / Zaker-Tabrizi, L. / Perugini, M.A. / Bottomley, S.P. / Coppel, R.L. / Crellin, P.K. / Rossjohn, J. / Beddoe, T.
History
DepositionMar 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5125
Polymers34,8271
Non-polymers6844
Water86548
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,02410
Polymers69,6552
Non-polymers1,3698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6270 Å2
ΔGint-46.6 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.967, 86.967, 103.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative uncharacterized protein


Mass: 34827.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium paratuberculosis (bacteria) / Strain: K-10 / References: UniProt: Q73WU1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 M Ammonium sulphate, 0.1 M HEPES pH 7.0, 20 mM Manganese chloride, 1 mM Sodium thiosulphate, 100 mM uridine-5 -diphosphate-N-acetyl-glucosamine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0053 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0053 Å / Relative weight: 1
ReflectionResolution: 2→43.48 Å / Num. all: 27634 / Num. obs: 26692 / Redundancy: 9.5 % / Rsym value: 0.077 / Net I/σ(I): 4.5
Reflection shellHighest resolution: 2 Å / Rsym value: 0.684

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Rigid body refinement / Resolution: 2→43.48 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.477 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24176 879 3.2 %RANDOM
Rwork0.22457 ---
obs0.22509 26692 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.082 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 38 48 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222391
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4322.0053295
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9985324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69223.18791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07615362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2621521
X-RAY DIFFRACTIONr_chiral_restr0.0870.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21064
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21589
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5731.51582
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99122489
X-RAY DIFFRACTIONr_scbond_it1.4223920
X-RAY DIFFRACTIONr_scangle_it2.0944.5794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 70 -
Rwork0.316 1949 -
obs--100 %
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)
17.2733-1.7241-0.42743.85763.59663.5673-0.3957-1.4987-0.81652.11120.5956-0.4491.57521.7463-0.19991.56750.47280.08470.09580.4667-0.034524.586612.263630.5114
21.2109-1.3325-1.36864.25480.6473.7509-0.406-0.332-0.16361.10430.01341.21070.654-0.620.39250.5036-0.09660.34990.1248-0.02020.41577.211426.844424.8123
32.0709-1.0082-1.08683.71421.73614.8217-0.2202-0.4196-0.15330.88220.19530.07050.68870.34720.02490.35750.0549-0.02640.11840.03160.210723.890123.045516.7405
40.9029-0.50792.62550.2857-1.47687.6344-0.61810.3304-0.67671.02550.24861.4480.8822-1.93210.36940.7125-0.10140.26980.18790.220.687210.879614.157814.13
53.3925-0.66950.73883.09221.51584.80430.1120.2999-0.1391-0.0911-0.27590.4304-0.1446-0.40530.16390.11080.0239-0.05940.1527-0.04260.309613.79327.9264-3.167
63.6840.52590.81015.75253.46068.52460.0737-0.30850.2120.460.00620.1259-0.4182-0.119-0.07990.28520.0110.02640.1036-0.0350.338917.052739.07615.5046
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 4815 - 48
2X-RAY DIFFRACTION2AA49 - 15649 - 156
3X-RAY DIFFRACTION3AA157 - 255157 - 255
4X-RAY DIFFRACTION4AA256 - 269256 - 269
5X-RAY DIFFRACTION5AA270 - 312270 - 312
6X-RAY DIFFRACTION6AA313 - 329313 - 329

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