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- PDB-6hvg: Crystal Structure of Truncated Alternansucrase from Leuconostoc m... -

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Basic information

Entry
Database: PDB / ID: 6hvg
TitleCrystal Structure of Truncated Alternansucrase from Leuconostoc mesenteroides NRRL B-1355
ComponentsAlternansucrase
KeywordsTRANSFERASE / GH70 / DEXTRAN / ALTERNAN / GLYCOSYLATION
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glucan-binding repeat / Glycoside hydrolase, family 70, catalytic domain / GW domain / GW domain superfamily / Glycosyl hydrolase family 70 / GW (Gly-Tryp) dipeptide domain / GW domain profile. / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat ...Glucan-binding repeat / Glycoside hydrolase, family 70, catalytic domain / GW domain / GW domain superfamily / Glycosyl hydrolase family 70 / GW (Gly-Tryp) dipeptide domain / GW domain profile. / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesLeuconostoc mesenteroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMolina, M. / Cioci, G. / Moulis, C. / Remaud-Simeon, M.
CitationJournal: Acs Catalysis / Year: 2019
Title: Deciphering an Undecided Enzyme: Investigations of the Structural Determinants Involved in the Linkage Specificity of Alternansucrase
Authors: Molina, M. / Moulis, C. / Monties, N. / Pizzut-Serin, S. / Guieysse, D. / Morel, S. / Cioci, G. / Remaud-Simeon, M.
History
DepositionOct 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Jan 24, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alternansucrase
B: Alternansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,5874
Polymers319,5072
Non-polymers802
Water5,008278
1
A: Alternansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7942
Polymers159,7531
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alternansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7942
Polymers159,7531
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.235, 134.804, 237.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 248 - 1422 / Label seq-ID: 234 - 1408

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alternansucrase


Mass: 159753.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc mesenteroides (bacteria) / Gene: asr / Plasmid: pet-53-dest / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9RE05, EC: 2.4.1.140
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.53 Å3/Da / Density % sol: 51.4 % / Description: rod
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG3350 14% 0.4M NaNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 27, 2017
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.8→47.82 Å / Num. obs: 80120 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 60.3 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.3
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11606 / CC1/2: 0.87 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LFC
Resolution: 2.8→47.82 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.918 / SU B: 29.683 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23732 4021 5 %RANDOM
Rwork0.20665 ---
obs0.2082 76019 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0 Å2
2---1.57 Å2-0 Å2
3---1.87 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19193 0 2 278 19473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0219599
X-RAY DIFFRACTIONr_bond_other_d0.0050.0217637
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9326572
X-RAY DIFFRACTIONr_angle_other_deg1.078340497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62252449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34525.6761036
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.613153160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1771567
X-RAY DIFFRACTIONr_chiral_restr0.0730.22813
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223298
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024811
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_it2.7584.7519805
X-RAY DIFFRACTIONr_mcbond_other2.7564.759804
X-RAY DIFFRACTIONr_mcangle_it4.4037.12712251
X-RAY DIFFRACTIONr_mcangle_other4.4037.12712252
X-RAY DIFFRACTIONr_scbond_it2.7774.8759794
X-RAY DIFFRACTIONr_scbond_other2.7764.8759794
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4377.22614322
X-RAY DIFFRACTIONr_long_range_B_refined7.6144.4984855
X-RAY DIFFRACTIONr_long_range_B_other7.60944.48884806
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 65919 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 312 -
Rwork0.295 5572 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.45460.366-0.1560.7476-0.16750.18410.0296-0.01240.07110.05260.00890.1031-0.0401-0.0874-0.03850.0258-0.01280.02630.1313-0.020.06676.47850.7732515.6449
20.7386-0.4799-0.37411.27150.25130.670.04260.1213-0.0242-0.0286-0.09670.1321-0.0671-0.1850.0540.01990.0040.01390.0831-0.0060.117811.4686-4.4516578.3633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A147 - 2000
2X-RAY DIFFRACTION2B248 - 2000

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