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- PDB-5rga: Crystal Structure of Kemp Eliminase HG3 with bound transition sta... -

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Basic information

Entry
Database: PDB / ID: 5rga
TitleCrystal Structure of Kemp Eliminase HG3 with bound transition state analogue, 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
6-NITROBENZOTRIAZOLE / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 1.3Nov 6, 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
B: Kemp Eliminase HG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4926
Polymers68,9712
Non-polymers5204
Water8,575476
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.240, 79.880, 99.050
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: 34485.742 Da / Num. of mol.: 2
Mutation: Q42M, T44W, R81G, H83G, T84M, 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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
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: 1.86→55.15 Å / Num. obs: 51523 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 17.584 Å2 / Rpim(I) all: 0.067 / Rrim(I) all: 0.238 / Net I/σ(I): 6.8 / Num. measured all: 656106
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
1.86-1.899.312348325130.3321.038
5.05-55.1811.716.33273227870.0290.103

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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: 1.86→55.15 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1863 1976 -
Rwork0.1482 --
obs-51523 99.05 %
Refinement stepCycle: final / Resolution: 1.86→55.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 42 483 5115
Biso mean--45.08 36.17 -
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 (%)
1.86-1.90650.30161380.27863415355398
1.9065-1.95810.27251440.23813424356899
1.9581-2.01570.26221350.2143436357199
2.0157-2.08080.24071360.19753430356699
2.0808-2.15510.21881340.17353474360899
2.1551-2.24140.20721440.16143465360999
2.2414-2.34350.2171450.15513456360199
2.3435-2.4670.19421400.15143510365099
2.467-2.62160.19311430.15613472361599
2.6216-2.8240.19891380.15313506364499
2.824-3.10810.1971430.150435283671100
3.1081-3.55780.16741420.131735673709100
3.5578-4.48220.13751460.099235873733100
4.4822-55.1760.14661480.13113735388399
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)
10.341-0.3232-0.01260.3655-0.10160.2172-0.0119-0.01960.04610.06920.00190.03810.0337-0.068300.18010.0112-0.00360.1384-0.00040.15259.164911.723233.4466
20.3828-0.2536-0.05180.24530.10520.37190.01560.0611-0.059-0.0623-0.00840.10.01060.02820.00020.17320.0151-0.00770.1472-0.0130.155313.32162.53419.2508
30.2481-0.07160.08730.21960.14480.18060.01050.13850.106-0.0085-0.0178-0.1387-0.00950.1223-0.00070.18610.03660.00650.2453-0.00320.166824.16621.845114.4403
40.7765-0.03540.20180.35810.4840.81350.04550.0647-0.05040.01250.0037-0.03630.17570.208200.19120.0405-0.0040.1761-0.02450.162627.6788-4.991325.8176
50.10290.0091-0.0910.09880.01730.08620.2136-0.1842-0.00330.164-0.0280.1074-0.0620.22480.0010.18920.0419-0.01560.2764-0.01180.213734.0271-5.32533.4444
60.6087-0.20830.11120.217-0.04470.422-0.0185-0.0193-0.01240.06950.040.00380.02340.081100.17890.0138-0.00580.16110.00050.151120.04162.388139.4108
70.3003-0.08170.29390.0877-0.00330.37550.0182-0.1196-0.07230.09650.04170.11110.0153-0.12470.00220.18930.0212-0.00510.1638-0.00530.16963.83224.282841.277
80.1669-0.12610.0770.2318-0.21710.2518-0.00690.0521-0.0640.00290.02510.03540.02880.014300.1792-0.00610.00890.1311-0.0060.1913-12.5536-11.293722.0465
90.16990.0667-0.15040.0692-0.12980.2469-0.00030.0856-0.04290.0055-0.0034-0.0615-0.0472-0.0223-00.19610.00480.00320.15880.00410.1841-0.8901-5.132412.7662
100.2128-0.0523-0.21780.04990.04950.22150.13420.10360.13920.0689-0.01810.1318-0.2189-0.08560.00010.28960.02620.03240.22750.03940.262-4.85634.87785.3967
110.32870.0396-0.25110.24130.05410.22040.05450.2771-0.0641-0.01940.0063-0.01-0.052-0.12720.00580.19690.03460.00610.29460.00810.1807-4.6405-1.6168-1.041
120.7290.262-0.41830.3743-0.08510.60470.18810.43770.1183-0.0358-0.1240.0578-0.1294-0.3048-0.04450.23870.07830.01230.31860.05040.222-15.96675.14691.3874
130.39660.7916-0.25521.5921-0.43680.6180.10410.45890.23120.0169-0.06590.3154-0.1708-0.35170.0450.25670.1097-0.04330.48210.04050.2642-26.68165.20390.5593
140.7642-0.23920.0220.2033-0.19770.45380.03240.1367-0.0102-0.0053-0.01520.0928-0.061-0.14760.00110.16510.0209-0.00520.1972-0.00050.2233-23.4509-1.636815.8714
150.4777-0.2024-0.04170.1035-0.01910.17890.008-0.16590.16640.1427-0.02140.1526-0.005-0.0747-00.1528-0.00090.01170.17090.00790.2154-16.0553-3.043830.1456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 31 )A3 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 100 )A32 - 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 31 )B3 - 31
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 76 )B32 - 76
10X-RAY DIFFRACTION10chain 'B' and (resid 77 through 100 )B77 - 100
11X-RAY DIFFRACTION11chain 'B' and (resid 101 through 130 )B101 - 130
12X-RAY DIFFRACTION12chain 'B' and (resid 131 through 181 )B131 - 181
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 196 )B182 - 196
14X-RAY DIFFRACTION14chain 'B' and (resid 197 through 270 )B197 - 270
15X-RAY DIFFRACTION15chain 'B' and (resid 271 through 303 )B271 - 303

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