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- PDB-3u48: From soil to structure: a novel dimeric family 3-beta-glucosidase... -

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Basic information

Entry
Database: PDB / ID: 3u48
TitleFrom soil to structure: a novel dimeric family 3-beta-glucosidase isolated from compost using metagenomic analysis
ComponentsJMB19063
KeywordsHYDROLASE / TIM Barrel / beta-d-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-D-glucopyranose
Similarity search - Component
Biological speciescompost metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 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)171,4126
Polymers170,9722
Non-polymers4404
Water14,988832
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-34 kcal/mol
Surface area49240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.488, 121.488, 242.859
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: 85485.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) compost metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium citrate and 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: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2009
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 92824 / Num. obs: 88156 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 15.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.73 / Num. unique all: 2993 / Rsym value: 0.612 / % possible all: 65.3

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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: 2.2→49.593 Å / SU ML: 0.54 / σ(F): 0 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 1690 2.26 %Random
Rwork0.169 ---
obs0.169 74931 80.77 %-
all-74931 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.856 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.1599 Å20 Å2-0 Å2
2--7.1599 Å2-0 Å2
3----14.3198 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11474 0 26 832 12332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511730
X-RAY DIFFRACTIONf_angle_d0.95715864
X-RAY DIFFRACTIONf_dihedral_angle_d12.5964351
X-RAY DIFFRACTIONf_chiral_restr0.0661770
X-RAY DIFFRACTIONf_plane_restr0.0042041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.26450.288870.24513775X-RAY DIFFRACTION51
2.2645-2.33760.29991050.24394461X-RAY DIFFRACTION60
2.3376-2.42120.34841140.23835215X-RAY DIFFRACTION70
2.4212-2.51810.28611250.20295520X-RAY DIFFRACTION74
2.5181-2.63270.26081310.19735870X-RAY DIFFRACTION79
2.6327-2.77150.23841450.19486065X-RAY DIFFRACTION81
2.7715-2.94510.24981370.19956159X-RAY DIFFRACTION82
2.9451-3.17250.2271440.18966595X-RAY DIFFRACTION87
3.1725-3.49170.23691720.17417094X-RAY DIFFRACTION94
3.4917-3.99670.18841730.14157221X-RAY DIFFRACTION95
3.9967-5.03470.16191720.12257366X-RAY DIFFRACTION96
5.0347-49.60590.19181850.15157900X-RAY DIFFRACTION98
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)
10.4897-0.26350.15650.5143-0.00241.45430.0322-0.08120.06850.10870.0054-0.0541-0.16640.0846-0.0320.2007-0.04820.00480.11690.0070.1494141.98972.764105.3306
21.2669-0.37950.33091.75460.26041.99160.0136-0.03420.03040.05150.0714-0.11160.01270.3075-0.08160.213-0.0352-0.01130.22720.00280.1458149.901364.4329110.2704
30.41770.00680.17650.5515-0.29780.922-0.0035-0.14780.14830.12530.0450.0965-0.4082-0.4683-0.04070.37070.14940.0610.3488-0.02120.199115.020885.3327100.3795
40.7344-0.0141-0.13750.3866-0.06791.19420.02890.00280.0995-0.01050.01110.0572-0.2253-0.2351-0.04440.21660.03860.00140.16750.02330.1419125.185479.395482.0658
52.8556-2.39821.40284.3533-0.27056.6741-0.24180.52940.1994-0.37230.1892-0.28380.03130.79030.04870.3427-0.10550.07890.30450.04180.2367153.959284.464666.6402
60.49370.15860.06810.4960.00371.31230.05570.1432-0.1571-0.10140.0194-0.03180.4860.1409-0.03970.35360.071-0.04340.157-0.02490.1691139.8645.580558.8816
70.75790.31040.15541.53750.60721.53640.05920.1442-0.1299-0.09640.0382-0.09420.23680.4779-0.07290.26080.0896-0.01010.2536-0.01510.1435149.763553.346654.6153
80.3340.22110.23260.33-0.25831.0676-0.00130.0867-0.2084-0.09820.09070.06630.5723-0.4351-0.00360.4666-0.2633-0.13920.3477-0.01580.1465112.169936.738763.0477
90.8954-0.0525-0.14060.3084-0.18030.78180.02010.2294-0.1209-0.05320.09730.15760.1878-0.6347-0.06490.2055-0.1434-0.06490.39730.04380.1505107.417850.089171.5033
100.3531-0.111-0.04140.362-0.02490.82180.0274-0.0239-0.2248-0.07320.03520.00340.4986-0.1324-0.06190.4402-0.06-0.05470.11010.03050.1459131.542236.790287.9079
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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