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- PDB-3klk: Crystal structure of Lactobacillus reuteri N-terminally truncated... -

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Basic information

Entry
Database: PDB / ID: 3klk
TitleCrystal structure of Lactobacillus reuteri N-terminally truncated glucansucrase GTF180 in triclinic apo- form
ComponentsGlucansucrase
KeywordsTRANSFERASE / native form / open conformation / multidomain protein / Glycosyltransferase
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glucansucrase / Cholin Binding / left handed beta-beta-3-solenoid / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. ...Glucansucrase / Cholin Binding / left handed beta-beta-3-solenoid / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Ribbon / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsVujicic-Zagar, A. / Pijning, T. / Kralj, S. / Eeuwema, W. / Dijkhuizen, L. / Dijkstra, B.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of a 117 kDa glucansucrase fragment provides insight into evolution and product specificity of GH70 enzymes
Authors: Vujicic-Zagar, A. / Pijning, T. / Kralj, S. / Lopez, C.A. / Eeuwema, W. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionNov 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Glucansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,51210
Polymers116,7361
Non-polymers7779
Water19,0061055
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.279, 65.949, 82.506
Angle α, β, γ (deg.)73.300, 78.460, 85.820
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glucansucrase


Mass: 116735.633 Da / Num. of mol.: 1
Fragment: N-terminally truncated GTF180, UNP residues 742-1772
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: 180 / Gene: gtf180 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SBN3, dextransucrase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1055 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONFLICT F1674L MAY DUE TO PCR ERROR.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5551.74
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, sodium potassium phosphate, BIS-TRIS propane-HCl buffer, pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.9791
SYNCHROTRONESRF ID2920.97911, 0.97927, 0.97564
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDDec 17, 2005
ADSC QUANTUM 315r2CCDDec 17, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.979111
30.979271
40.975641
ReflectionResolution: 1.65→77.625 Å / Num. obs: 133854 / % possible obs: 96.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.743.70.4531.571015192130.45394.8
1.74-1.843.80.2972.270393183030.29795.5
1.84-1.973.80.1932.866229173190.19395.9
1.97-2.133.80.1294.661543161950.12996.4
2.13-2.333.80.0975.756240149380.09796.9
2.33-2.613.70.0786.950660135310.07897.3
2.61-3.013.70.077.744662120350.0797.8
3.01-3.693.60.0638.736949102220.06398.2
3.69-5.223.40.05111.22675178750.05198.5
5.22-63.123.60.04114.91534442230.04195.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALA3.2.21data scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.861 / SU B: 4.103 / SU ML: 0.072 / SU R Cruickshank DPI: 0.109 / SU Rfree: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 6715 5 %RANDOM
Rwork0.165 ---
obs0.167 133798 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 102.23 Å2 / Biso mean: 22.596 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0.53 Å20.68 Å2
2--0.1 Å2-0.14 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7977 0 49 1055 9081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0228205
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.93511151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13451009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85325.459436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.689151308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7441535
X-RAY DIFFRACTIONr_chiral_restr0.120.21188
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026426
X-RAY DIFFRACTIONr_nbd_refined0.2260.24138
X-RAY DIFFRACTIONr_nbtor_refined0.3220.25716
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2937
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3470.248
X-RAY DIFFRACTIONr_mcbond_it5.3581.55111
X-RAY DIFFRACTIONr_mcangle_it5.32128029
X-RAY DIFFRACTIONr_scbond_it7.55633591
X-RAY DIFFRACTIONr_scangle_it7.8944.53120
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 506 -
Rwork0.262 9221 -
all-9727 -
obs--94.65 %
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)
10.36771.599-1.17688.7122-3.66684.9608-0.14780.0325-0.09350.23560.0327-0.45410.11430.06350.1151-0.0001-0.0001-0.000100.00010.000143.71892.1247.424
20.66860.5031-0.56320.8368-0.26731.1128-0.02570.0661-0.004-0.04640.0343-0.0046-0.1015-0.0339-0.0086-0.1011-0.01970.0154-0.12950.0067-0.192716.16528.75175.659
31.0393-1.70050.92662.7902-1.38463.0074-0.018-0.1131-0.15260.08430.12160.23940.1929-0.096-0.10350.0606-0.14010.09040.01990.06680.000744.75591.54934.392
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A746 - 815
2X-RAY DIFFRACTION2A816 - 1640
3X-RAY DIFFRACTION3A1641 - 1751

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