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- PDB-5rg5: Crystal Structure of Kemp Eliminase HG3.3b in unbound state, 277K -

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Basic information

Entry
Database: PDB / ID: 5rg5
TitleCrystal Structure of Kemp Eliminase HG3.3b in unbound state, 277K
ComponentsKemp Eliminase HG3
KeywordsHYDROLASE
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / 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: 1.62 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 16, 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

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Assembly

Deposited unit
A: Kemp Eliminase HG3
B: Kemp Eliminase HG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5687
Polymers69,1622
Non-polymers4065
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-30 kcal/mol
Surface area21050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.230, 80.030, 98.910
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


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-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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
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: 1.62→37.09 Å / Num. obs: 77569 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 14.716 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.169 / Net I/σ(I): 8.9 / Num. measured all: 998006
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
1.62-1.6510.914180138340.4071.368
4.4-37.11227.24995241680.020.07

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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: 1.62→37.09 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1665 1993 -
Rwork0.1421 --
obs-77569 99.78 %
Refinement stepCycle: final / Resolution: 1.62→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 29 462 5095
Biso mean--74.22 35.99 -
Num. residues----602
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 (%)
1.62-1.66050.25421340.26625297543199
1.6605-1.70540.27311310.243353325463100
1.7054-1.75560.25151530.220152945447100
1.7556-1.81230.24491340.193653355469100
1.8123-1.8770.19991450.171853055450100
1.877-1.95220.1961480.158453535501100
1.9522-2.0410.16791360.151452945430100
2.041-2.14860.17261400.137153725512100
2.1486-2.28320.14371450.129953705515100
2.2832-2.45950.17381400.128653885528100
2.4595-2.70690.14941450.141253995544100
2.7069-3.09850.16481440.147454295573100
3.0985-3.9030.14841440.124854845628100
3.903-37.10410.14461540.117456825836100
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)
10.6358-0.3174-0.00260.2064-0.14970.4828-0.03940.03080.00630.03820.01370.0593-0.0008-0.0328-00.16550.0135-0.00240.12040.00120.15919.090311.559732.2357
20.616-0.6233-0.02020.9466-0.04240.15860.04240.1321-0.1487-0.1024-0.07180.18930.0369-0.01970.00040.19480.0203-0.00920.1722-0.02970.186514.7127-0.119416.8137
30.2866-0.00950.2030.5018-0.10760.42080.04760.19690.0575-0.0728-0.0738-0.08440.03690.1055-0.00040.18860.0310.0090.2331-0.00320.172823.97022.34815.0201
40.7931-0.20860.10470.32270.29490.97720.04750.0604-0.06560.0163-0.0212-0.00750.16170.155200.18580.0339-0.00390.1685-0.01330.155827.6974-4.884425.6715
50.1925-0.0423-0.16640.08340.05990.1490.1939-0.0905-0.01850.16630.03090.0011-0.00580.22310.00180.17020.0375-0.0180.2426-0.0130.200534.7753-4.829332.9303
60.6336-0.2430.06860.3930.01030.6585-0.0215-0.1005-0.03690.06150.0375-0.01390.01440.080500.16930.0137-0.00220.15440.00520.15519.51962.250738.7594
70.655-0.2120.41290.3197-0.11360.49630.0621-0.1301-0.09310.0703-0.02620.02630.0371-0.091900.1790.02010.00240.15560.0020.16374.54963.929840.9819
80.2957-0.32070.1390.4168-0.08470.56660.00070.0636-0.05830.00370.03110.02240.01050.0245-00.1618-0.00230.00270.12620.00090.1789-11.102-10.55421.5147
90.39830.0722-0.30440.432-0.06920.41540.07160.08910.06040.02330.01430.058-0.1485-0.02720.00020.20260.00910.01330.17610.01840.1834-1.72520.43118.2622
100.85250.1703-0.60690.3607-0.09250.78540.12290.32130.0668-0.0699-0.04670.0428-0.1443-0.16730.05660.20910.0520.00770.25940.02450.1689-9.61412.9527-1.2797
110.87870.5381-0.31230.3945-0.3110.33350.10780.30310.1197-0.0305-0.07990.134-0.1318-0.306200.23650.0747-0.01610.32750.01090.2073-22.52523.18544.1758
120.8673-0.1715-0.07150.21470.13210.48790.03330.115-0.0267-0.0335-0.02030.0994-0.0431-0.17210.0030.1630.019-0.00340.1893-0.00190.1982-22.8177-1.726915.8553
130.6609-0.30290.09620.2725-0.01770.2778-0.0064-0.16420.12750.1294-0.01410.0589-0.0399-0.049700.14460.00310.01370.16430.01160.1782-16.0783-2.898529.8588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 45 )A3 - 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 303 )A271 - 303
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 45 )B3 - 45
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 100 )B46 - 100
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 163 )B101 - 163
11X-RAY DIFFRACTION11chain 'B' and (resid 164 through 196 )B164 - 196
12X-RAY DIFFRACTION12chain 'B' and (resid 197 through 270 )B197 - 270
13X-RAY DIFFRACTION13chain 'B' and (resid 271 through 303 )B271 - 303

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