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- PDB-5z87: Structural of a novel b-glucosidase EmGH1 at 2.3 angstrom from Er... -

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Basic information

Entry
Database: PDB / ID: 5z87
TitleStructural of a novel b-glucosidase EmGH1 at 2.3 angstrom from Erythrobacter marinus
ComponentsEmGH1
KeywordsHYDROLASE / EmGH1 / Glucoside hydrolase / Erythrobacter marinus
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Twin arginine translocation (Tat) signal profile. ...Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
BENZAMIDINE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / DI(HYDROXYETHYL)ETHER / Fn3_like domain-containing protein
Similarity search - Component
Biological speciesErythrobacter marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, J.X. / Hu, X.J. / Zhao, Y. / Li, L.
CitationJournal: To Be Published
Title: Structural and biochemical analysis of a novel b-glucosidase EmGH1 from Erythrobacter marinus
Authors: Li, L. / Zhao, Y. / Hu, X.J. / Li, J.X.
History
DepositionJan 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EmGH1
B: EmGH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,83228
Polymers168,7502
Non-polymers2,08226
Water18,4111022
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-13 kcal/mol
Surface area47480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.640, 132.150, 194.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein EmGH1


Mass: 84375.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacter marinus (bacteria) / Gene: AAV99_00160 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H0XV02

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Non-polymers , 7 types, 1048 molecules

#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1022 / 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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350, 0.05M magnesium acetate, 2% benzamidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 99834 / % possible obs: 99.93 % / Redundancy: 14 % / Biso Wilson estimate: 35 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.138 / Χ2: 0.943 / Net I/σ(I): 22.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 3.87 / Num. unique obs: 4956 / CC1/2: 0.938 / Rpim(I) all: 0.2 / Rrim(I) all: 0.753 / Χ2: 0.743 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata reduction
HKL-2000data scaling
PHASERphasing
PHENIX(1.12_2829: ???)refinement
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U48

3u48


Resolution: 2.3→43.32 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.63
RfactorNum. reflection% reflection
Rfree0.2116 4961 4.97 %
Rwork0.1617 --
obs0.1642 99762 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11442 0 130 1022 12594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711927
X-RAY DIFFRACTIONf_angle_d0.85716157
X-RAY DIFFRACTIONf_dihedral_angle_d10.6939769
X-RAY DIFFRACTIONf_chiral_restr0.0511748
X-RAY DIFFRACTIONf_plane_restr0.0062193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.27691480.20533141X-RAY DIFFRACTION100
2.3261-2.35350.2461880.19673088X-RAY DIFFRACTION100
2.3535-2.38220.26141660.17933088X-RAY DIFFRACTION100
2.3822-2.41240.25171780.18273158X-RAY DIFFRACTION100
2.4124-2.44410.24221600.18363097X-RAY DIFFRACTION100
2.4441-2.47760.25991620.18343197X-RAY DIFFRACTION100
2.4776-2.5130.24721520.18163079X-RAY DIFFRACTION100
2.513-2.55050.23261700.18613140X-RAY DIFFRACTION100
2.5505-2.59030.22541550.18323136X-RAY DIFFRACTION100
2.5903-2.63280.23821830.17823140X-RAY DIFFRACTION100
2.6328-2.67820.28231530.2133101X-RAY DIFFRACTION100
2.6782-2.72690.26471450.19153173X-RAY DIFFRACTION100
2.7269-2.77930.20671510.17193140X-RAY DIFFRACTION100
2.7793-2.8360.27791820.17413117X-RAY DIFFRACTION100
2.836-2.89770.23551560.17983160X-RAY DIFFRACTION100
2.8977-2.96510.22461640.17943119X-RAY DIFFRACTION100
2.9651-3.03920.26971370.18253190X-RAY DIFFRACTION100
3.0392-3.12140.24681740.18113122X-RAY DIFFRACTION100
3.1214-3.21320.24951850.1763163X-RAY DIFFRACTION100
3.2132-3.31690.23381490.16633158X-RAY DIFFRACTION100
3.3169-3.43540.20181870.16343155X-RAY DIFFRACTION100
3.4354-3.57280.19631680.16253154X-RAY DIFFRACTION100
3.5728-3.73540.20941780.16363143X-RAY DIFFRACTION100
3.7354-3.93220.2171540.15653177X-RAY DIFFRACTION100
3.9322-4.17840.17311830.12743169X-RAY DIFFRACTION100
4.1784-4.50070.1581690.12023183X-RAY DIFFRACTION100
4.5007-4.9530.15021870.12033185X-RAY DIFFRACTION100
4.953-5.66840.16811510.13163238X-RAY DIFFRACTION100
5.6684-7.13640.16521680.14453280X-RAY DIFFRACTION100
7.1364-43.32770.18451580.15643410X-RAY DIFFRACTION100

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