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

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Basic information

Entry
Database: PDB / ID: 3ckj
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
CITRIC ACID / PHOSPHATE ION / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 15, 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 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 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)35,4696
Polymers34,8271
Non-polymers6425
Water1,838102
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,93812
Polymers69,6552
Non-polymers1,28310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7450 Å2
ΔGint-105 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.6, 86.6, 104.3
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.6 M mono-Ammonium dihydrogen phosphate, 0.1 M Sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9793, 0.9794, 0.9641, 1.0
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97941
30.96411
411
ReflectionResolution: 1.8→100 Å / Num. all: 37229 / Num. obs: 35916 / Redundancy: 4.6 % / Rsym value: 0.03
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.505

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.412 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20124 1158 3.1 %RANDOM
Rwork0.19011 ---
obs0.19046 35916 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 42 102 2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222384
X-RAY DIFFRACTIONr_angle_refined_deg1.5682.0073282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5715318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92322.96791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1715362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0891522
X-RAY DIFFRACTIONr_chiral_restr0.1010.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021812
X-RAY DIFFRACTIONr_nbd_refined0.2130.21164
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2146
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.214
X-RAY DIFFRACTIONr_mcbond_it0.9591.51565
X-RAY DIFFRACTIONr_mcangle_it1.41622473
X-RAY DIFFRACTIONr_scbond_it2.363918
X-RAY DIFFRACTIONr_scangle_it3.5814.5800
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 87 -
Rwork0.296 2616 -
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)
115.05431.9777-2.48552.97043.04224.5971-0.5641-0.3296-0.11741.07630.38480.28510.98731.01520.17940.91490.3623-0.03570.12090.22170.158826.20997.326823.1954
23.0931-1.2890.60824.68520.27084.0177-0.3836-0.5225-0.1761.13780.13760.92680.6617-0.14570.2460.5267-0.02450.32290.15430.10570.14779.630521.824528.4576
32.84760.7334-1.35136.0615-0.72414.0461-0.0422-0.45020.01710.63980.04160.88-0.2176-0.38390.00070.18360.06230.09640.093-0.07550.3096.056937.444520.7474
41.5082-1.1722-0.47254.0881-0.71142.9066-0.2602-0.4616-0.04450.73910.11610.52160.1962-0.22090.14420.24290.02070.09820.0728-0.00050.135512.161629.598123.5026
54.1014-0.4285-1.74974.9046-0.50794.5377-0.3028-0.608-0.38181.03730.16550.29830.77620.26280.13720.64760.13650.09370.16810.12070.195519.079716.563126.1864
61.4323-0.9842-0.66853.07071.31113.5011-0.1261-0.219-0.08140.38750.09720.12360.28380.11630.02890.15510.0118-0.03610.05340.01310.119922.537424.448313.7173
76.34773.2681-0.86687.9402-0.18334.0544-0.2791-0.4128-0.02770.78360.2539-0.04930.49590.57140.02520.39760.1597-0.06040.14430.0330.095425.83720.07120.6647
80.5972-1.76643.79775.2246-11.23324.1511-0.29190.3257-0.70520.82590.01570.73570.9558-0.99560.27620.3724-0.13310.09660.23740.09820.60375.976616.78139.81
93.8072-0.13011.67922.61440.88324.18070.03330.1597-0.0951-0.0709-0.11270.2814-0.0866-0.19460.07940.08650.0083-0.04720.069-0.02530.189813.733528.1154-2.9756
104.3242-0.09950.4996.97073.13199.1271-0.0821-0.51580.28090.7160.07440.0359-0.23380.10290.00770.2620.0025-0.03570.0611-0.07490.23218.494741.290319.3539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 2615 - 26
2X-RAY DIFFRACTION2AA27 - 9827 - 98
3X-RAY DIFFRACTION3AA99 - 12099 - 120
4X-RAY DIFFRACTION4AA121 - 143121 - 143
5X-RAY DIFFRACTION5AA144 - 172144 - 172
6X-RAY DIFFRACTION6AA173 - 244173 - 244
7X-RAY DIFFRACTION7AA245 - 261245 - 261
8X-RAY DIFFRACTION8AA262 - 268262 - 268
9X-RAY DIFFRACTION9AA269 - 315269 - 315
10X-RAY DIFFRACTION10AA316 - 329316 - 329

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