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

ID or keywords:

Entry

Database: PDB / ID: 5rgb

Title

Crystal Structure of Kemp Eliminase HG3.3b with bound transition state analogue, 277K

Components

Kemp Eliminase HG3.3b

Keywords

HYDROLASE

Function / homology

Function and homology information

endo-1,4-beta-xylanase activity /

endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function

Biological species

Thermoascus aurantiacus (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.42 Å

Authors

Broom, A. / Rakotoharisoa, R.V. / Thompson, M.C. / Fraser, J.S. / Chica, R.A.

Funding support

Canada, 1items

Citation

Journal: 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

Deposition	Mar 19, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 2, 2020	Group: 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 1.2	May 12, 2021	Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rg/5rgb ftp://data.pdbj.org/pub/pdb/validation_reports/rg/5rgb	HTTPS FTP

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Group deposition

ID	G_1002148 (12 entries) 5rg4 5rg5 5rg6 5rg7 5rg8 5rg9 5rga 5rgb 5rgc 5rgd
Title	Crystal structures of HG-series of Kemp Eliminases at Room-temperature
Type	undefined
Description	Crystal structure of Kemp eliminase HG3.3b with bound transition state analogue, 277K

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Related structure data

Similar structure data	5rge-d 5rg9-2 7k4p-2 6tu6-11 7k4z-d 5rg9-1 6tu6-9 7k4w-d 7k4q-2 6srw-2 6tu6-16 6ss1-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#217 - Jan 2018 Opioid Receptors similarity (1)

Deposited unit

A: Kemp Eliminase HG3.3b

B: Kemp Eliminase HG3.3b

hetero molecules

69.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Kemp Eliminase HG3.3b

hetero molecules

defined by author
34.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Kemp Eliminase HG3.3b

hetero molecules

defined by author
34.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	19
Space group name H-M	P2₁2₁2₁

#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 / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.42 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 277 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 1.1158 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1158 Å / Relative weight: 1

Reflection

Resolution: 1.42→48.16 Å / Num. obs: 113916 / % possible obs: 99.8 % / Redundancy: 6.4 % / B_iso Wilson estimate: 14.847 Å² / R_pim(I) all: 0.043 / R_rim(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) obs	Num. measured all	Num. unique obs	R_pim(I) all	R_rim(I) all	% possible all
1.42-1.44	6.4	1.1	36300	5630	0.54	1.38	99.8
3.85-48.18	6.1	25.9	36718	6024	0.022	0.056	99.6

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
xia2		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.42→48.16 Å / Cross valid method: FREE R-VALUE

	R_factor	Num. reflection	% reflection
R_free	0.1668	2010	-
R_work	0.136	-	-
obs	-	113916	99.72 %

Refinement step

Cycle: final / Resolution: 1.42→48.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4570	0	47	497	5114
B_iso mean	-	-	53.04	36.3	-
Num. residues	-	-	-	-	597

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.42-1.4555	0.333	140	0.2719	7916	8056	100
1.4555-1.4949	0.2831	153	0.2425	7931	8084	100
1.4949-1.5389	0.2288	133	0.2189	7903	8036	100
1.5389-1.5885	0.2432	138	0.1983	7878	8016	100
1.5885-1.6453	0.1979	154	0.1811	7925	8079	100
1.6453-1.7112	0.2147	129	0.1676	7942	8071	100
1.7112-1.7891	0.1667	154	0.1513	7943	8097	100
1.7891-1.8834	0.1531	134	0.1376	7923	8057	100
1.8834-2.0014	0.1626	147	0.1244	8010	8157	100
2.0014-2.156	0.1676	142	0.1175	7967	8109	100
2.156-2.3729	0.1358	146	0.1146	7991	8137	100
2.3729-2.7163	0.159	144	0.123	8058	8202	100
2.7163-3.4221	0.1547	144	0.1329	8092	8236	100
3.4221-48.1828	0.1518	152	0.1178	8338	8490	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.4411	-0.3427	-0.0625	0.4114	-0.1847	0.382	-0.0553	0.0586	0.0096	0.0366	0.0281	0.0217	0.0016	0.0252	-0	0.1608	0.0122	-0.0033	0.1248	0.0008	0.152	9.1498	11.8325	32.2126
2	0.5489	-0.4508	0.0969	0.5278	-0.0995	0.25	0.0564	0.1289	-0.1295	-0.0799	-0.0833	0.1709	0.0554	0.0117	0.0005	0.1903	0.0261	-0.007	0.1605	-0.0282	0.1727	15.0075	-1.1018	16.0006
3	0.3265	-0.0453	0.1851	0.2567	-0.1628	0.4307	0.0325	0.169	0.0708	-0.0547	-0.0402	-0.0852	0.0283	0.1679	-0.0025	0.1701	0.0308	0.0089	0.2209	-0.0071	0.1563	23.9954	2.1057	14.5696
4	0.6248	-0.2116	0.155	0.2178	0.2565	0.7472	0.0444	0.0478	-0.0468	0.0159	-0.0118	-0.0361	0.1596	0.181	0.0007	0.173	0.0386	-0.004	0.1573	-0.0132	0.1472	27.729	-4.3611	25.5568
5	0.1235	-0.088	-0.1146	0.0759	0.0849	0.1061	0.1454	-0.1789	0.0342	0.1319	0.0395	-0.0029	0.0753	0.349	0.0002	0.1646	0.0406	-0.0116	0.2557	-0.0118	0.1895	34.3683	-4.9659	33.4014
6	0.6138	-0.2395	0.1647	0.2001	-0.017	0.5228	-0.0463	-0.0761	-0.0161	0.0508	0.057	-0.0168	0.0369	0.0786	-0	0.1672	0.018	-0.0009	0.1567	-0.0001	0.1504	19.702	1.9649	38.9963
7	0.4891	-0.2083	0.314	0.1567	-0.0619	0.362	0.0534	-0.1431	-0.1273	0.1012	-0.0086	0.024	0.0629	-0.0938	0.0002	0.1648	0.0254	-0.0025	0.1514	0.0032	0.1476	3.8176	2.9254	40.1634
8	0.2006	-0.2918	0.0204	0.5018	-0.0745	0.4207	-0.0145	0.0723	-0.0525	-0.0013	0.0333	0.0389	-0.0083	0.0526	0.0006	0.1519	-0.0012	0.002	0.1163	-0.0008	0.1762	-10.7927	-10.7603	21.4065
9	0.4057	0.0682	-0.3436	0.3505	-0.0388	0.425	0.0897	0.0829	0.0488	0.0619	-0.0035	0.0425	-0.1683	-0.0305	0.0002	0.2032	0.0127	0.0175	0.1633	0.0203	0.1792	-1.2729	1.7427	7.6714
10	0.7757	0.2666	-0.6284	0.2944	-0.0062	0.7788	0.1417	0.2848	0.055	-0.0412	-0.0689	0.0042	-0.154	-0.1166	0.0744	0.2004	0.0497	0.0107	0.2296	0.0243	0.1566	-8.529	3.4745	0.1056
11	0.5579	0.1071	0.0096	0.1715	-0.159	0.332	0.1129	0.3853	0.0287	-0.0227	-0.1237	0.0809	-0.1078	-0.2655	-0.0105	0.1957	0.0525	-0.0003	0.2569	0.0038	0.1797	-16.535	0.4852	2.2003
12	0.346	0.565	-0.2485	0.9239	-0.425	0.6531	0.1205	0.4132	0.0441	-0.1066	0.0265	0.2377	-0.1281	-0.3399	0.2676	0.2358	0.1241	-0.0399	0.4474	0.0228	0.192	-26.3704	5.0211	-0.064
13	1.2467	-0.3039	0.0413	0.4011	-0.0294	0.6164	0.0065	0.0244	0.0053	-0.009	-0.0143	0.0813	-0.0564	-0.1304	0.0012	0.13	0.0113	0.0062	0.1467	0.0043	0.1716	-20.2249	-1.7755	21.2217

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 45 )	A	4 - 45
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 100 )	A	46 - 100
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 101 through 130 )	A	101 - 130
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 131 through 181 )	A	131 - 181
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 182 through 196 )	A	182 - 196
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 197 through 270 )	A	197 - 270
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 271 through 302 )	A	271 - 302
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 4 through 45 )	B	4 - 45
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 46 through 100 )	B	46 - 100
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 101 through 149 )	B	101 - 149
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 150 through 181 )	B	150 - 181
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 182 through 197 )	B	182 - 197
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 198 through 302 )	B	198 - 302

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