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- PDB-6ms3: Crystal structure of the GH43 protein BlXynB mutant (K247S) from ... -

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Basic information

Entry
Database: PDB / ID: 6ms3
TitleCrystal structure of the GH43 protein BlXynB mutant (K247S) from Bacillus licheniformis
ComponentsGlycoside Hydrolase Family 43
KeywordsHYDROLASE / glycoside hydrolase / GH43 / Bacillus lincheniformis
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Glycoside Hydrolase Family 43
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZanphorlin, L.M. / Morais, M.A.B. / Diogo, J.A. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: Biotechnol. Bioeng. / Year: 2019
Title: Structure-guided design combined with evolutionary diversity led to the discovery of the xylose-releasing exo-xylanase activity in the glycoside hydrolase family 43.
Authors: Zanphorlin, L.M. / de Morais, M.A.B. / Diogo, J.A. / Domingues, M.N. / de Souza, F.H.M. / Ruller, R. / Murakami, M.T.
History
DepositionOct 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside Hydrolase Family 43
B: Glycoside Hydrolase Family 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,31419
Polymers120,8542
Non-polymers1,45917
Water12,088671
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-155 kcal/mol
Surface area36030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.126, 82.126, 173.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycoside Hydrolase Family 43


Mass: 60427.156 Da / Num. of mol.: 2 / Mutation: K247S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46) (bacteria)
Strain: ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46
Gene: xynB, BL03023 / Production host: Escherichia coli (E. coli) / References: UniProt: Q65MB6

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Non-polymers , 5 types, 688 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M imidazole pH 6.5, 26% (v/v) MPD, 10% (v/v) PEG3350, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.95→48.234 Å / Num. obs: 82290 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 31.21 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.124 / Χ2: 0.98 / Net I/σ(I): 10.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-2.071.131.54131820.5071.2598.1
2.07-2.210.7182.48124240.7480.79498.4
2.21-2.390.463.88115760.8710.50898.5
2.39-2.610.3015.75106720.9410.33399
2.61-2.920.1729.6997400.9810.1999.1
2.92-3.370.08817.4885890.9940.09899.4
3.37-4.120.05427.1773210.9970.0699.6
4.12-5.810.04332.8756660.9980.04799.9
5.81-48.2340.03734.1831750.9980.04199.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10_2148refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.23 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.13 / Phase error: 20.8
RfactorNum. reflection% reflection
Rfree0.2009 3919 2.42 %
Rwork0.1676 --
obs0.1684 82290 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.25 Å2 / Biso mean: 34.7666 Å2 / Biso min: 19.76 Å2
Refinement stepCycle: final / Resolution: 1.95→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8149 0 79 671 8899
Biso mean--61.86 39.66 -
Num. residues----1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038506
X-RAY DIFFRACTIONf_angle_d0.68611578
X-RAY DIFFRACTIONf_chiral_restr0.0481171
X-RAY DIFFRACTIONf_plane_restr0.0041511
X-RAY DIFFRACTIONf_dihedral_angle_d16.9894890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9495-1.97330.30791410.31645575571696
1.9733-1.99830.29071320.30115674580698
1.9983-2.02460.27221460.28935523566998
2.0246-2.05230.33551390.2715645578497
2.0523-2.08160.31911380.27615608574697
2.0816-2.11270.30221400.26325651579198
2.1127-2.14570.29951360.25775538567498
2.1457-2.18090.25741320.24145624575698
2.1809-2.21850.3011370.2355652578998
2.2185-2.25880.20851430.21565565570897
2.2588-2.30230.22751460.2155630577698
2.3023-2.34930.2591390.20675740587998
2.3493-2.40030.24621400.20525604574498
2.4003-2.45620.19711370.19175612574998
2.4562-2.51760.20481480.1935720586898
2.5176-2.58570.22081440.18255609575398
2.5857-2.66170.20051440.18175681582599
2.6617-2.74760.23141400.18185651579198
2.7476-2.84580.22661400.17095630577098
2.8458-2.95980.22431410.16785635577699
2.9598-3.09440.23611440.16135756590099
3.0944-3.25750.15911410.15355691583299
3.2575-3.46160.19311520.14695676582898
3.4616-3.72880.19031360.13265752588899
3.7288-4.10380.13041440.12365669581399
4.1038-4.69720.12791450.10975726587199
4.6972-5.91630.17711240.12615732585699
5.9163-48.24940.19721300.15365604573497
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)
12.27271.3286-2.01951.4996-1.17862.7601-0.10450.2066-0.0613-0.0860.0685-0.00640.2978-0.13680.040.32110.0506-0.02020.2583-0.00120.258814.1371.98-2.956
22.58130.0461-0.72362.5171-0.22071.7738-0.01330.0451-0.3402-0.0047-0.0181-0.13950.49670.04950.02440.46160.0806-0.01440.23420.02170.332318.50358.5434.883
33.23870.5534-0.25282.99220.90134.3142-0.12930.3319-0.4926-0.02570.1126-0.43780.68170.38070.00130.53060.15220.02790.37410.01380.565233.0557.1180.519
42.2719-0.5537-0.85452.87250.62280.9826-0.0425-0.1114-0.19910.1499-0.0519-0.45980.23560.26590.0680.29350.0984-0.04960.38760.0640.369436.28474.076.431
51.43070.4334-0.17370.7463-0.03940.60890.01460.1409-0.0488-0.0168-0.0067-0.02030.14750.0287-0.00230.2620.0339-0.0170.22150.01180.200212.40676.2150.98
61.4845-0.2220.09931.2139-0.09991.32710.0258-0.1008-0.06880.0795-0.0190.14690.1956-0.1683-0.0080.2866-0.01920.00470.25890.01270.2389-5.48977.64313.425
71.87451.84811.18582.91990.71961.1349-0.08720.0436-0.0427-0.07870.0701-0.1664-0.05380.0150.01360.26170.04320.00750.26580.00240.3034-18.253104.3-11.49
81.50660.73030.43372.67810.69662.6927-0.13590.04560.3031-0.14420.03880.0602-0.3177-0.04220.13320.32720.0634-0.06010.2484-0.0020.3867-20.627118.441-10.196
92.36551.062-1.04580.717-0.24855.4398-0.1111-0.10190.5417-0.11920.11690.2606-0.50060.07050.01550.36590.0633-0.10340.25730.01160.4435-25.198121.296-13.049
102.29020.0309-0.79432.7597-0.37082.9077-0.20170.21610.4351-0.12570.1110.318-0.3431-0.3140.07870.34610.0654-0.12020.35990.03470.5058-37.068118.793-16.294
111.78580.17960.78761.6627-1.25371.7864-0.0818-0.21320.32390.05530.13790.3027-0.1674-0.2362-0.06050.24070.0878-0.00120.3587-0.03840.4073-40.411106.937-2.283
121.36480.56220.4790.9698-0.00050.958-0.0265-0.0277-0.0468-0.10240.03240.01940.0011-0.05680.00020.21550.03510.00350.2583-0.00670.2874-26.58295.743-4.467
133.8776-0.0634-0.36551.4005-0.92762.8509-0.05210.25140.2599-0.1636-0.0731-0.2456-0.11640.06120.10890.2991-0.004-0.00550.220.03650.3050.704114.291-8.536
142.85920.83810.51532.0967-0.04531.8594-0.0389-0.12840.205-0.0139-0.0687-0.1763-0.22030.04890.10850.25120.0206-0.00950.22460.00570.25821.742110.1624.098
152.3482-0.0724-0.13750.91920.01981.6803-0.0379-0.15260.11290.0391-0.0333-0.0752-0.14050.05870.06720.23510.0137-0.01980.2279-0.00080.25471.517106.6346.247
168.48021.09180.19868.6861-2.80648.8493-0.0197-0.3938-0.2785-0.01430.1801-0.39020.0758-0.0019-0.13960.23120.01690.00180.2574-0.00030.238-4.41993.8350.895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 28:55 )A28 - 55
2X-RAY DIFFRACTION2( CHAIN A AND RESID 56:139 )A56 - 139
3X-RAY DIFFRACTION3( CHAIN A AND RESID 140:169 )A140 - 169
4X-RAY DIFFRACTION4( CHAIN A AND RESID 170:238 )A170 - 238
5X-RAY DIFFRACTION5( CHAIN A AND RESID 239:362 )A239 - 362
6X-RAY DIFFRACTION6( CHAIN A AND RESID 363:515 )A363 - 515
7X-RAY DIFFRACTION7( CHAIN B AND RESID 28:55 )B28 - 55
8X-RAY DIFFRACTION8( CHAIN B AND RESID 56:101 )B56 - 101
9X-RAY DIFFRACTION9( CHAIN B AND RESID 102:139 )B102 - 139
10X-RAY DIFFRACTION10( CHAIN B AND RESID 140:169 )B140 - 169
11X-RAY DIFFRACTION11( CHAIN B AND RESID 170:238 )B170 - 238
12X-RAY DIFFRACTION12( CHAIN B AND RESID 239:318 )B239 - 318
13X-RAY DIFFRACTION13( CHAIN B AND RESID 319:362 )B319 - 362
14X-RAY DIFFRACTION14( CHAIN B AND RESID 363:423 )B363 - 423
15X-RAY DIFFRACTION15( CHAIN B AND RESID 424:511 )B424 - 511
16X-RAY DIFFRACTION16( CHAIN B AND RESID 512:515 )B512 - 515

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