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- PDB-5rg9: Crystal Structure of Kemp Eliminase HG4 in unbound state, 277K -

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Basic information

Entry
Database: PDB / ID: 5rg9
TitleCrystal Structure of Kemp Eliminase HG4 in unbound state, 277K
ComponentsKemp Eliminase HG4
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
ACETATE ION / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kemp Eliminase HG4
B: Kemp Eliminase HG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0676
Polymers68,7572
Non-polymers3104
Water8,449469
1
A: Kemp Eliminase HG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5343
Polymers34,3791
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kemp Eliminase HG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5343
Polymers34,3791
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.290, 79.990, 98.980
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 HG4


Mass: 34378.602 Da / Num. of mol.: 2
Mutation: Q42M, T44W, K50Q, R81G, G82A, H83G, M84C, Q90F, A125T, N130G, N172M, A234S, T236L, E237M, F267M, W275A, R276F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Gene: XYNA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23360, endo-1,4-beta-xylanase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 43.99 %
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: 1.47→79.99 Å / Num. obs: 103164 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 14.072 Å2 / Rpim(I) all: 0.048 / Rrim(I) all: 0.117 / Net I/σ(I): 8.2 / Num. measured all: 601193
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.47-1.55.91.12993351010.551.34899.6
3.99-80.115.523.23002854990.0250.059100

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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: 1.47→79.99 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1633 1989 -
Rwork0.1434 --
obs-103164 99.64 %
Refinement stepCycle: final / Resolution: 1.47→79.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 24 474 5056
Biso mean--58.61 37.1 -
Num. residues----599
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 (%)
1.47-1.50680.35231350.293271207255100
1.5068-1.54750.29681380.27047127726599
1.5475-1.59310.27571450.246871567301100
1.5931-1.64450.25851410.23637120726199
1.6445-1.70330.25221420.222671887330100
1.7033-1.77150.22681370.198871467283100
1.7715-1.85210.17851400.160971717311100
1.8521-1.94970.14821400.135571907330100
1.9497-2.07190.1541480.12671777325100
2.0719-2.23190.14561480.117272447392100
2.2319-2.45650.11741370.117372527389100
2.4565-2.81190.14351430.130972697412100
2.8119-3.54270.16541480.138473397487100
3.5427-60.47560.1351470.119375817728100
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)
10.8786-0.2220.19050.4007-0.22130.2932-0.05740.10580.03410.0390.03930.0484-0.01020.0242-0.00190.16860.0118-0.00350.1029-0.00520.15229.076411.490731.9266
20.339-0.3206-0.05350.7129-0.13960.28420.09690.166-0.0683-0.1589-0.0860.07160.06130.0310.01280.20720.0457-0.03020.1703-0.04020.172714.6593-0.062515.815
30.3481-0.00790.18740.2306-0.04410.30310.07620.28120.068-0.1296-0.0938-0.06470.02430.2092-0.00910.19320.05460.0090.2503-0.00970.153424.30161.74814.2948
40.8666-0.15690.24360.4150.21810.91120.08060.099-0.0519-0.0135-0.0523-0.05060.12240.2428-0.00040.17130.0533-0.0040.1729-0.01760.149727.9641-4.340125.4334
50.1714-0.1466-0.13180.08930.07820.04550.1594-0.1634-0.09890.1046-0.00060.00080.06940.3451-0.00010.16720.0481-0.02080.2797-0.01390.197234.5337-5.209333.2746
60.8984-0.31980.24880.33240.02450.6587-0.0304-0.1067-0.05590.05890.0447-0.01220.00170.053300.16460.0209-0.00090.12760.00270.135215.00242.838939.6687
70.5353-0.37260.08790.4846-0.08360.5093-0.02590.1226-0.06430.0060.04780.04820.0120.01560.00720.1679-0.0070.00460.11430.00180.1938-11.4606-10.751221.2655
80.50210.0542-0.21010.38260.21380.41010.05740.18830.0294-0.06140.0069-0.012-0.0452-0.03330.00990.17910.00820.01290.18750.03670.1883-1.19160.20288.2021
90.3488-0.1438-0.07890.17710.06610.16290.06790.3954-0.0558-0.0926-0.0536-0.0134-0.0096-0.0530.01670.19940.02930.01310.32920.0160.1844-4.7582-1.7537-1.0571
100.74030.2514-0.34930.79240.13640.64380.1530.48850.1369-0.0743-0.11330.1098-0.1486-0.3206-0.13760.20380.08670.00940.340.05860.1966-16.2255.64581.7726
110.19760.3389-0.15880.6476-0.21670.27380.0740.46540.28930.08520.05170.1760.0954-0.30860.09040.25550.1031-0.04130.55550.0490.2674-26.35975.11570.2916
121.4669-0.22680.00230.4487-0.07890.76770.00970.0838-0.00430.0026-0.00080.1089-0.0386-0.18660.00080.14630.01440.00750.17510.00290.2033-20.948-2.284120.1488
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 303 )A197 - 303
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 45 )B4 - 45
8X-RAY DIFFRACTION8chain 'B' and (resid 46 through 100 )B46 - 100
9X-RAY DIFFRACTION9chain 'B' and (resid 101 through 130 )B101 - 130
10X-RAY DIFFRACTION10chain 'B' and (resid 131 through 181 )B131 - 181
11X-RAY DIFFRACTION11chain 'B' and (resid 182 through 197 )B182 - 197
12X-RAY DIFFRACTION12chain 'B' and (resid 198 through 303 )B198 - 303

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