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- PDB-5rgb: Crystal Structure of Kemp Eliminase HG3.3b with bound transition ... -

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Basic information

Entry
Database: PDB / ID: 5rgb
TitleCrystal Structure of Kemp Eliminase HG3.3b with bound transition state analogue, 277K
ComponentsKemp Eliminase HG3.3b
KeywordsHYDROLASE
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
6-NITROBENZOTRIAZOLE / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsBroom, A. / Rakotoharisoa, R.V. / Thompson, M.C. / Fraser, J.S. / Chica, R.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council of Canada Canada
CitationJournal: Nat Commun / Year: 2020
Title: Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico.
Authors: Broom, A. / Rakotoharisoa, R.V. / Thompson, M.C. / Zarifi, N. / Nguyen, E. / Mukhametzhanov, N. / Liu, L. / Fraser, J.S. / Chica, R.A.
History
DepositionMar 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 12, 2021Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kemp Eliminase HG3.3b
B: Kemp Eliminase HG3.3b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7787
Polymers69,1622
Non-polymers6165
Water8,773487
1
A: Kemp Eliminase HG3.3b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8413
Polymers34,5811
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kemp Eliminase HG3.3b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9374
Polymers34,5811
Non-polymers3563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.240, 79.920, 98.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kemp Eliminase HG3.3b


Mass: 34580.781 Da / Num. of mol.: 2
Mutation: V6I, Q42M, T44W, K50H, R81G, H83G, T84C, S89R, Q90D, A125N, N130G, N172M, A234S, T236L, E237M, W267F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23360, endo-1,4-beta-xylanase
#2: Chemical ChemComp-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.8-2.4 M Ammonium Sulfate, 4mg/mL Protein Concentration, 100mM Sodium Acetate
PH range: 4.5-5.0

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.42→48.16 Å / Num. obs: 113916 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.847 Å2 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Net I/σ(I): 8.9 / Num. measured all: 729351
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.42-1.446.41.13630056300.541.3899.8
3.85-48.186.125.93671860240.0220.05699.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
xia2data scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→48.16 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1668 2010 -
Rwork0.136 --
obs-113916 99.72 %
Refinement stepCycle: final / Resolution: 1.42→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 47 497 5114
Biso mean--53.04 36.3 -
Num. residues----597
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.42-1.45550.3331400.271979168056100
1.4555-1.49490.28311530.242579318084100
1.4949-1.53890.22881330.218979038036100
1.5389-1.58850.24321380.198378788016100
1.5885-1.64530.19791540.181179258079100
1.6453-1.71120.21471290.167679428071100
1.7112-1.78910.16671540.151379438097100
1.7891-1.88340.15311340.137679238057100
1.8834-2.00140.16261470.124480108157100
2.0014-2.1560.16761420.117579678109100
2.156-2.37290.13581460.114679918137100
2.3729-2.71630.1591440.12380588202100
2.7163-3.42210.15471440.132980928236100
3.4221-48.18280.15181520.11788338849099
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)
10.4411-0.3427-0.06250.4114-0.18470.382-0.05530.05860.00960.03660.02810.02170.00160.0252-00.16080.0122-0.00330.12480.00080.1529.149811.832532.2126
20.5489-0.45080.09690.5278-0.09950.250.05640.1289-0.1295-0.0799-0.08330.17090.05540.01170.00050.19030.0261-0.0070.1605-0.02820.172715.0075-1.101816.0006
30.3265-0.04530.18510.2567-0.16280.43070.03250.1690.0708-0.0547-0.0402-0.08520.02830.1679-0.00250.17010.03080.00890.2209-0.00710.156323.99542.105714.5696
40.6248-0.21160.1550.21780.25650.74720.04440.0478-0.04680.0159-0.0118-0.03610.15960.1810.00070.1730.0386-0.0040.1573-0.01320.147227.729-4.361125.5568
50.1235-0.088-0.11460.07590.08490.10610.1454-0.17890.03420.13190.0395-0.00290.07530.3490.00020.16460.0406-0.01160.2557-0.01180.189534.3683-4.965933.4014
60.6138-0.23950.16470.2001-0.0170.5228-0.0463-0.0761-0.01610.05080.057-0.01680.03690.0786-00.16720.018-0.00090.1567-0.00010.150419.7021.964938.9963
70.4891-0.20830.3140.1567-0.06190.3620.0534-0.1431-0.12730.1012-0.00860.0240.0629-0.09380.00020.16480.0254-0.00250.15140.00320.14763.81762.925440.1634
80.2006-0.29180.02040.5018-0.07450.4207-0.01450.0723-0.0525-0.00130.03330.0389-0.00830.05260.00060.1519-0.00120.0020.1163-0.00080.1762-10.7927-10.760321.4065
90.40570.0682-0.34360.3505-0.03880.4250.08970.08290.04880.0619-0.00350.0425-0.1683-0.03050.00020.20320.01270.01750.16330.02030.1792-1.27291.74277.6714
100.77570.2666-0.62840.2944-0.00620.77880.14170.28480.055-0.0412-0.06890.0042-0.154-0.11660.07440.20040.04970.01070.22960.02430.1566-8.5293.47450.1056
110.55790.10710.00960.1715-0.1590.3320.11290.38530.0287-0.0227-0.12370.0809-0.1078-0.2655-0.01050.19570.0525-0.00030.25690.00380.1797-16.5350.48522.2003
120.3460.565-0.24850.9239-0.4250.65310.12050.41320.0441-0.10660.02650.2377-0.1281-0.33990.26760.23580.1241-0.03990.44740.02280.192-26.37045.0211-0.064
131.2467-0.30390.04130.4011-0.02940.61640.00650.02440.0053-0.009-0.01430.0813-0.0564-0.13040.00120.130.01130.00620.14670.00430.1716-20.2249-1.775521.2217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 45 )A4 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 100 )A46 - 100
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 130 )A101 - 130
4X-RAY DIFFRACTION4chain 'A' and (resid 131 through 181 )A131 - 181
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 196 )A182 - 196
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 270 )A197 - 270
7X-RAY DIFFRACTION7chain 'A' and (resid 271 through 302 )A271 - 302
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 45 )B4 - 45
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 100 )B46 - 100
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 149 )B101 - 149
11X-RAY DIFFRACTION11chain 'B' and (resid 150 through 181 )B150 - 181
12X-RAY DIFFRACTION12chain 'B' and (resid 182 through 197 )B182 - 197
13X-RAY DIFFRACTION13chain 'B' and (resid 198 through 302 )B198 - 302

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