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- PDB-3oka: Crystal structure of Corynebacterium glutamicum PimB' in complex ... -

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Basic information

Entry
Database: PDB / ID: 3oka
TitleCrystal structure of Corynebacterium glutamicum PimB' in complex with GDP-Man (triclinic crystal form)
Components
  • GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
  • N-terminal His-affinity tag
KeywordsTRANSFERASE / GT-B fold / alpha-mannosyltransferase / GDP-Man binding
Function / homology
Function and homology information


phosphatidyl-myo-inositol dimannoside synthase / glycolipid 1,6-alpha-mannosyltransferase activity / phosphatidylinositol alpha-mannosyltransferase activity / UDP-sulfoquinovose:DAG sulfoquinovosyltransferase activity / sulfolipid biosynthetic process / glycolipid biosynthetic process / phospholipid biosynthetic process / phosphatidylinositol metabolic process
Similarity search - Function
Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / GDP-mannose-dependent monoacylated alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsBatt, S.M. / Jabeen, T. / Besra, G.S. / Futterer, K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Acceptor substrate discrimination in phosphatidyl-myo-inositol mannoside synthesis: structural and mutational analysis of mannosyltransferase Corynebacterium glutamicum PimB'.
Authors: Batt, S.M. / Jabeen, T. / Mishra, A.K. / Veerapen, N. / Krumbach, K. / Eggeling, L. / Besra, G.S. / Futterer, K.
History
DepositionAug 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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

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Assembly

Deposited unit
A: GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
B: GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
C: N-terminal His-affinity tag
D: N-terminal His-affinity tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,11917
Polymers87,8564
Non-polymers2,26313
Water5,296294
1
A: GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
C: N-terminal His-affinity tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0098
Polymers43,9282
Non-polymers1,0826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
D: N-terminal His-affinity tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1109
Polymers43,9282
Non-polymers1,1827
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.070, 50.020, 85.300
Angle α, β, γ (deg.)92.05, 92.68, 89.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 381
2111B1 - 381
1121C-20 - -7
2121D-20 - -7

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase / Guanosine diphosphomannose-phosphatidyl-inositol alpha-mannosyltransferase / Phosphatidylinositol ...Guanosine diphosphomannose-phosphatidyl-inositol alpha-mannosyltransferase / Phosphatidylinositol alpha-mannosyltransferase / PI alpha-mannosyltransferase / Alpha-mannosyltransferase / Alpha-manT / Alpha-D-mannose-alpha-(1-6)-phosphatidylmyo-inositol-mannosyltransferase


Mass: 41376.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: pimB, Cgl2186, cg2400 / Plasmid: pET16b / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NNK8, phosphatidylinositol alpha-mannosyltransferase
#2: Protein/peptide N-terminal His-affinity tag


Mass: 2551.749 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: His-affinity tag / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 307 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsAUTHORS EXPLAIN THAT THE EXPRESSION TAGS ARE NOT CLEAVED, BUT THERE IS NO CONTINUOUS DENSITY ...AUTHORS EXPLAIN THAT THE EXPRESSION TAGS ARE NOT CLEAVED, BUT THERE IS NO CONTINUOUS DENSITY BETWEEN THE C-TERMINAL RESIDUE OF THE TAG AND THE N-TERMINUS OF THE ACTUAL PROTEIN SEQUENCE. WHILE A BIT ARBITRARY, THE AUTHORS GAVE THE SEQUENCE TAGS SEPARATE CHAIN IDS. IT WAS NOT POSSIBLE TO DETERMINE TO WHICH OF THE TWO PROTEIN CHAINS (A OR B) TAG-CHAINS C AND D BELONGED

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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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 6-26% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.1 M lithium sulfate and 0.1 M glycine, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2008
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→43.8 Å / Num. all: 35191 / Num. obs: 35191 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 5.9 / Num. unique all: 4400 / Rsym value: 0.238 / % possible all: 81.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→43.8 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.427 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.218
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1747 5 %RANDOM
Rwork0.18937 ---
all0.19097 33243 --
obs0.19097 33243 94.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.213 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0.23 Å2-0.14 Å2
2---0.94 Å20.09 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 112 294 6231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216061
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9718273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2195777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53722.739230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18615920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6821545
X-RAY DIFFRACTIONr_chiral_restr0.0790.2956
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024521
X-RAY DIFFRACTIONr_nbd_refined0.1860.22537
X-RAY DIFFRACTIONr_nbtor_refined0.2950.24118
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2345
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.224
X-RAY DIFFRACTIONr_mcbond_it0.4081.53975
X-RAY DIFFRACTIONr_mcangle_it0.69126231
X-RAY DIFFRACTIONr_scbond_it1.16732352
X-RAY DIFFRACTIONr_scangle_it1.9614.52042
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2788tight positional0.030.05
2C91tight positional0.070.05
1A2788tight thermal0.050.5
2C91tight thermal0.10.5
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 86 -
Rwork0.208 1836 -
obs--71.03 %

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