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- PDB-6gdt: Crystal structure of exo-glucosidase/glucosaminidase VC0615 from ... -

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Basic information

Entry
Database: PDB / ID: 6gdt
TitleCrystal structure of exo-glucosidase/glucosaminidase VC0615 from Vibrio Cholerae
ComponentsEndoglucanase-related protein
KeywordsCARBOHYDRATE / Hydrolase / Glucosaminidase / Glucosidase / GH9
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set ...Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Endoglucanase-related protein
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsWu, L. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-32294 United Kingdom
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structure of the GH9 glucosidase/glucosaminidase from Vibrio cholerae.
Authors: Wu, L. / Davies, G.J.
History
DepositionApr 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Endoglucanase-related protein
B: Endoglucanase-related protein
C: Endoglucanase-related protein
D: Endoglucanase-related protein
E: Endoglucanase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,0856
Polymers331,0235
Non-polymers621
Water1,27971
1
A: Endoglucanase-related protein

D: Endoglucanase-related protein


Theoretical massNumber of molelcules
Total (without water)132,4092
Polymers132,4092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-y,x-y-1,z-1/31
Buried area2670 Å2
ΔGint-14 kcal/mol
Surface area37190 Å2
MethodPISA
2
C: Endoglucanase-related protein
hetero molecules

B: Endoglucanase-related protein


Theoretical massNumber of molelcules
Total (without water)132,4713
Polymers132,4092
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area2930 Å2
ΔGint-10 kcal/mol
Surface area37210 Å2
MethodPISA
3
E: Endoglucanase-related protein


Theoretical massNumber of molelcules
Total (without water)66,2051
Polymers66,2051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.899, 234.899, 129.421
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 566 / Label seq-ID: 1 - 566

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15BB
25CC
16BB
26DD
17BB
27EE
18CC
28DD
19CC
29EE
110DD
210EE

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Endoglucanase-related protein


Mass: 66204.633 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_0615 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9KUA8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Tris pH 7.5, 5% PGA-LM, 8% PEG 20k

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.17→47.33 Å / Num. obs: 69816 / % possible obs: 100 % / Redundancy: 11.5 % / Biso Wilson estimate: 74 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.08 / Net I/σ(I): 8.4
Reflection shellResolution: 3.17→3.24 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4464 / CC1/2: 0.322 / Rpim(I) all: 0.904 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H7L

3h7l


Resolution: 3.17→47.33 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.873 / SU B: 26.946 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R Free: 0.528 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27978 3411 4.9 %RANDOM
Rwork0.23534 ---
obs0.23742 66351 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 103.012 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å2-0 Å2
2---0.3 Å20 Å2
3---0.97 Å2
Refinement stepCycle: 1 / Resolution: 3.17→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22634 0 4 71 22709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01423271
X-RAY DIFFRACTIONr_bond_other_d0.0010.01819985
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.64731613
X-RAY DIFFRACTIONr_angle_other_deg0.8591.73546357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20152820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91424.281250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.951153601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.16615120
X-RAY DIFFRACTIONr_chiral_restr0.0550.22869
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0226630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025170
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_it7.95310.53911298
X-RAY DIFFRACTIONr_mcbond_other7.94610.53911297
X-RAY DIFFRACTIONr_mcangle_it12.19215.80914112
X-RAY DIFFRACTIONr_mcangle_other12.19215.8114113
X-RAY DIFFRACTIONr_scbond_it7.61610.7111973
X-RAY DIFFRACTIONr_scbond_other7.61610.7111973
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.85915.97217502
X-RAY DIFFRACTIONr_long_range_B_refined15.53926937
X-RAY DIFFRACTIONr_long_range_B_other15.53926938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A200550.06
12B200550.06
21A201960.06
22C201960.06
31A200290.06
32D200290.06
41A195280.08
42E195280.08
51B200020.06
52C200020.06
61B200210.06
62D200210.06
71B194880.08
72E194880.08
81C200380.06
82D200380.06
91C195240.08
92E195240.08
101D194160.09
102E194160.09
LS refinement shellResolution: 3.17→3.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 240 -
Rwork0.356 4848 -
obs--99.76 %

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