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- PDB-3u4a: From soil to structure: a novel dimeric family 3-beta-glucosidase... -

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Basic information

Entry
Database: PDB / ID: 3u4a
TitleFrom soil to structure: a novel dimeric family 3-beta-glucosidase isolated from compost using metagenomic analysis
ComponentsJMB19063
KeywordsHYDROLASE / TIM Barrel / 3-beta-glucosidase
Function / homology
Function and homology information


Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / beta-D-glucopyranose
Similarity search - Component
Biological speciescompost metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å
AuthorsMcAndrew, R.P. / Park, J.I. / Reindl, W. / Friedland, G.D. / D'haeseleer, P. / Northen, T. / Sale, K.L. / Simmons, B.A. / Adams, P.D.
CitationJournal: To be Published
Title: From soil to structure: a novel dimeric family 3-beta--glucosidase isolated from compost using metagenomic analysis
Authors: McAndrew, R.P. / Park, J.I. / Reindl, W. / Friedland, G.D. / D'haeseleer, P. / Northen, T. / Sale, K.L. / Simmons, B.A. / Adams, P.D.
History
DepositionOct 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JMB19063
B: JMB19063
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0557
Polymers170,9702
Non-polymers1,0855
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-18 kcal/mol
Surface area49100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.748, 121.748, 242.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein JMB19063 / 3-beta-glucosidase


Mass: 85484.812 Da / Num. of mol.: 2 / Mutation: D261N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) compost metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium citrate, 30% (w/v) PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2010
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.196→50 Å / Num. all: 93681 / Num. obs: 93226 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 20.6
Reflection shellResolution: 2.196→2.24 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.48 / Num. unique all: 4355 / Rsym value: 0.649 / % possible all: 94.7

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.196→49.68 Å / SU ML: 0.58 / σ(F): 1.33 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1978 2.14 %Random
Rwork0.1877 ---
obs0.1877 92293 98.55 %-
all-92293 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.567 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.6331 Å20 Å2-0 Å2
2--10.6331 Å2-0 Å2
3----21.2662 Å2
Refinement stepCycle: LAST / Resolution: 2.196→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11474 0 71 482 12027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511778
X-RAY DIFFRACTIONf_angle_d0.92115934
X-RAY DIFFRACTIONf_dihedral_angle_d12.6024351
X-RAY DIFFRACTIONf_chiral_restr0.0641790
X-RAY DIFFRACTIONf_plane_restr0.0042041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.196-2.25080.29281320.28546051X-RAY DIFFRACTION94
2.2508-2.31170.36071380.27096300X-RAY DIFFRACTION98
2.3117-2.37970.28081420.25066399X-RAY DIFFRACTION99
2.3797-2.45650.29531390.23636425X-RAY DIFFRACTION99
2.4565-2.54430.28871410.22556470X-RAY DIFFRACTION100
2.5443-2.64620.26421430.22036453X-RAY DIFFRACTION100
2.6462-2.76660.28431410.2266435X-RAY DIFFRACTION99
2.7666-2.91240.25741410.23256412X-RAY DIFFRACTION99
2.9124-3.09490.23341420.22886443X-RAY DIFFRACTION99
3.0949-3.33380.28171420.21836457X-RAY DIFFRACTION99
3.3338-3.66920.21981390.18916501X-RAY DIFFRACTION99
3.6692-4.19990.19871440.15216450X-RAY DIFFRACTION97
4.1999-5.29040.14681420.13356572X-RAY DIFFRACTION98
5.2904-49.69290.18191520.1566947X-RAY DIFFRACTION100
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)
10.5469-0.10030.23330.6565-0.17312.30190.0406-0.08710.09060.1311-0.002-0.0495-0.23920.0841-0.02970.3661-0.04110.00490.2138-0.00150.27142.353672.9275105.313
21.6944-0.91270.38264.17560.9922.87360.0315-0.07690.06690.13770.0729-0.22170.03790.3637-0.11040.3444-0.0546-0.01490.29830.02330.2161150.282364.6011110.2173
30.74130.05790.41531.0726-0.3621.36310.0238-0.17430.15080.22420.03110.1727-0.4064-0.5775-0.04540.54410.18560.09120.5373-0.00630.3324115.402785.4804100.4382
40.8184-0.0516-0.140.6164-0.08661.61110.03540.03840.1421-0.02840.01550.1056-0.2588-0.3538-0.050.34460.0770.00160.25140.02130.2293125.535479.621382.0988
54.6404-3.11122.03415.3282-1.11877.7806-0.27631.21070.7522-0.2022-0.225-0.4363-0.02811.34630.45890.4604-0.05460.07640.48010.10120.3186154.355384.668366.7779
60.56230.18640.19570.4789-0.07651.65780.11040.2007-0.184-0.1709-0.016-0.05650.64090.1054-0.06760.62570.116-0.04770.3041-0.05230.2995140.209145.868558.8324
71.36790.49870.06443.06741.08711.09210.06860.1714-0.2078-0.18860.0756-0.17640.30690.5138-0.1450.5390.1757-0.01540.421-0.01810.2795150.084653.626654.6022
80.54290.15320.38361.0098-0.13680.90940.16380.2909-0.1011-0.23360.03210.04290.625-0.7649-0.01580.8338-0.3246-0.20730.6457-0.0410.3649112.583536.949463.0011
92.68530.24310.65550.97690.22460.60640.03710.1296-0.0879-0.04650.05840.17130.211-0.8407-0.09310.4813-0.1444-0.09090.63630.03040.3177107.771150.246771.4816
100.7716-0.3564-0.13840.8492-0.39571.24560.0503-0.0583-0.2132-0.13920.04980.02290.6979-0.1627-0.07010.6373-0.0825-0.09510.18030.00830.2311131.94136.989187.8056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:249)
2X-RAY DIFFRACTION2(chain A and resid 250:342)
3X-RAY DIFFRACTION3(chain A and resid 343:437)
4X-RAY DIFFRACTION4(chain A and resid 438:731)
5X-RAY DIFFRACTION5(chain A and resid 732:739)
6X-RAY DIFFRACTION6(chain B and resid 2:248)
7X-RAY DIFFRACTION7(chain B and resid 249:339)
8X-RAY DIFFRACTION8(chain B and resid 340:437)
9X-RAY DIFFRACTION9(chain B and resid 438:537)
10X-RAY DIFFRACTION10(chain B and resid 538:743)

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