PDB-7k4x: Crystal structure of Kemp Eliminase HG3.7 in complex with the tra...

ID or keywords:

Entry

Database: PDB / ID: 7k4x

Title

Crystal structure of Kemp Eliminase HG3.7 in complex with the transition state analog 6-nitrobenzotriazole

Components

Endo-1,4-beta-xylanase

Keywords

HYDROLASE / kemp elimination / directed evolution / transition state analog

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: 1.6 Å

Authors

Padua, R.A.P. / Otten, R. / Bunzel, A. / Nguyen, V. / Pitsawong, W. / Patterson, M. / Sui, S. / Perry, S.L. / Cohen, A.E. / Hilvert, D. / Kern, D.

Funding support

United States,

Switzerland, 11items

Organization	Grant number	Country
Department of Energy (DOE, United States)	DE-FG02-05ER15699	United States
Damon Runyon Cancer Research Foundation	DRG-2114-12	United States
Department of Energy (DOE, United States)	DE-AC02-76SF00515	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P41GM103393	United States
Howard Hughes Medical Institute (HHMI)		United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P30 GM124169	United States
Department of Energy (DOE, United States)	DE-AC02-05CH11231	United States
National Institutes of Health/Office of the Director	S10OD021832	United States
Swiss National Science Foundation		Switzerland
Other government		Switzerland
National Science Foundation (NSF, United States)	BioXFEL STC (1231306)	United States

Citation

Journal: Science / Year: 2020
Title: How directed evolution reshapes the energy landscape in an enzyme to boost catalysis.
Authors: Otten, R. / Padua, R.A.P. / Bunzel, H.A. / Nguyen, V. / Pitsawong, W. / Patterson, M. / Sui, S. / Perry, S.L. / Cohen, A.E. / Hilvert, D. / Kern, D.

History

Deposition	Sep 16, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 2, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 30, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7k4x.cif.gz	432.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7k4x.ent.gz	294.9 KB	Display	PDB format
PDBx/mmJSON format	7k4x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7k4x_validation.pdf.gz	472.7 KB	Display	wwPDB validaton report
Full document	7k4x_full_validation.pdf.gz	473.5 KB	Display
Data in XML	7k4x_validation.xml.gz	28.1 KB	Display
Data in CIF	7k4x_validation.cif.gz	42.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k4/7k4x ftp://data.pdbj.org/pub/pdb/validation_reports/k4/7k4x	HTTPS FTP

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Related structure data

Related structure data	7k4pC 7k4qC 7k4rC 7k4sC 7k4tC 7k4uC 7k4vC 7k4wC 7k4yC 7k4zC 4bs0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7k4q-1 6tu6-9 1i1w-d 5h2u-3 1gor-d 1b31-d 6tu6-15 1b3z-d 1b3y-d 1gok-d 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: Endo-1,4-beta-xylanase

B: Endo-1,4-beta-xylanase

hetero molecules

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

1

A: Endo-1,4-beta-xylanase

hetero molecules

defined by author&software
Evidence: gel filtration
34 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Endo-1,4-beta-xylanase

hetero molecules

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

Unit cell

Length a, b, c (Å)	75.170, 77.330, 97.090
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Endo-1,4-beta-xylanase / Xylanase / 1 / 4-beta-D-xylan xylanohydrolase / TAXI Mass: 33309.480 Da / Num. of mol.: 2 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-6NT / 6-NITROBENZOTRIAZOLE Mass: 164.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₄N₄O₂
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 41.92 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium acetate trihydrate, pH 4.6, and 2 M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.8855 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8855 Å / Relative weight: 1
Reflection	Resolution: 1.6→41.11 Å / Num. obs: 75249 / % possible obs: 99.96 % / Redundancy: 2 % / B_iso Wilson estimate: 17.94 Å² / CC_1/2: 0.997 / Net I/σ(I): 5.93
Reflection shell	Resolution: 1.6→1.657 Å / Num. unique obs: 7438 / CC_1/2: 0.428

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Processing

Software

Name	Version	Classification
PHENIX	dev_3965	refinement
Coot		model building
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4bs0

4bs0

Resolution: 1.6→41.11 Å / SU ML: 0.2647 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2275	3838	2.68 %
R_work	0.1956	139308	-
obs	0.1965	75233	99.22 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 24.67 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→41.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4609	0	70	512	5191

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0044	4893
X-RAY DIFFRACTION	f_angle_d	0.7608	6695
X-RAY DIFFRACTION	f_chiral_restr	0.0461	743
X-RAY DIFFRACTION	f_plane_restr	0.0057	875
X-RAY DIFFRACTION	f_dihedral_angle_d	6.4762	666

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6-1.62	0.4142	138	0.3958	4851	X-RAY DIFFRACTION	93.8
1.62-1.64	0.3955	141	0.3867	4918	X-RAY DIFFRACTION	94.56
1.64-1.66	0.3951	118	0.3703	5021	X-RAY DIFFRACTION	96.58
1.66-1.69	0.395	151	0.3726	5077	X-RAY DIFFRACTION	97.14
1.69-1.71	0.3841	146	0.3688	5103	X-RAY DIFFRACTION	98.65
1.71-1.74	0.3781	132	0.3397	5223	X-RAY DIFFRACTION	99.63
1.74-1.77	0.3286	150	0.3117	5169	X-RAY DIFFRACTION	99.81
1.77-1.8	0.3579	145	0.2944	5213	X-RAY DIFFRACTION	99.94
1.8-1.83	0.3079	130	0.2736	5216	X-RAY DIFFRACTION	99.94
1.83-1.87	0.2834	141	0.2707	5164	X-RAY DIFFRACTION	99.94
1.87-1.9	0.289	157	0.2485	5189	X-RAY DIFFRACTION	99.94
1.9-1.95	0.2675	150	0.2369	5165	X-RAY DIFFRACTION	99.96
1.95-1.99	0.287	136	0.233	5234	X-RAY DIFFRACTION	99.94
1.99-2.04	0.2832	146	0.2284	5217	X-RAY DIFFRACTION	99.96
2.04-2.1	0.2548	145	0.2156	5192	X-RAY DIFFRACTION	99.93
2.1-2.16	0.2378	145	0.188	5173	X-RAY DIFFRACTION	99.89
2.16-2.23	0.2334	127	0.1824	5203	X-RAY DIFFRACTION	99.94
2.23-2.31	0.2422	144	0.1797	5188	X-RAY DIFFRACTION	99.96
2.31-2.4	0.2429	156	0.1695	5203	X-RAY DIFFRACTION	100
2.4-2.51	0.2014	135	0.177	5221	X-RAY DIFFRACTION	99.96
2.51-2.64	0.2068	147	0.1743	5185	X-RAY DIFFRACTION	99.66
2.64-2.81	0.1981	139	0.1772	5156	X-RAY DIFFRACTION	99.87
2.81-3.02	0.201	138	0.1661	5242	X-RAY DIFFRACTION	100
3.02-3.33	0.2188	145	0.1627	5173	X-RAY DIFFRACTION	100
3.33-3.81	0.1556	149	0.1406	5220	X-RAY DIFFRACTION	100
3.81-4.8	0.1373	139	0.1263	5183	X-RAY DIFFRACTION	99.94
4.8-41.11	0.1804	148	0.1682	5209	X-RAY DIFFRACTION	99.98

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	3.75645140036	0.121975906544	1.37765451715	1.67438739393	0.0472771691267	2.55236528763	-0.125981097338	-0.136618445489	0.0787145997834	0.185191606891	0.0154903567951	-0.0457181390381	-0.147564569346	0.0768061813911	0.10321732631	0.16035658209	0.0182928869093	-0.0265111501881	0.0947804543921	0.0306260149303	0.107456804299	8.53753203962	11.8809424096	32.1737786607
2	0.72013162638	-0.708054384792	-0.220353899488	2.10118789971	1.00790860848	1.8423036151	-0.0160247807115	0.0506797823836	-0.0469092384113	0.00748390723525	-0.0265384418088	-0.0157266322875	0.160815411088	0.192378226666	0.0442922010338	0.159877977733	0.0142495972078	0.00354317258093	0.19027523959	0.0151856398675	0.145500402803	14.4037323733	0.253741119926	16.3224337867
3	0.452459558337	0.157137611847	0.4811620079	1.74818018232	-0.135463962696	2.35327460873	-0.0577109573447	0.0890048127827	-0.0208397536744	-0.036333812573	0.0379109292993	-0.129028750156	0.0658706390261	0.411377204032	0.00255191453528	0.106086103422	0.00179730381088	0.00809958737696	0.289332733818	0.0168117503753	0.147340875952	23.5436907434	2.28899338886	14.7547636139
4	0.512990516379	0.0540928061958	0.264050021621	0.791418229902	-0.131395776268	3.35206237395	0.20845197942	0.175200349828	-0.16691571489	-0.139958924394	-0.00737506001208	-0.081789754729	0.509813203907	0.223949051429	-0.0444737766714	0.258865894679	0.127054688448	-0.0154417291795	0.265652943549	-0.010286493891	0.198184060882	26.8030448461	-13.3532901748	24.3397674949
5	0.27956756946	0.228452673577	-0.720979618809	6.11889001859	-1.24473754962	4.02457428931	-0.00679421081491	-0.0898072204086	0.0694388878625	0.184813522117	0.129301978786	-0.249951373207	-0.0757244029061	0.52477940777	0.0594179598053	0.159484525698	0.0171194892347	-0.00492848116642	0.347181512615	0.00720644740044	0.192554359082	31.7499537031	-0.810043004287	18.7191514776
6	0.941033138355	0.751805809855	-0.77897088808	1.95010284282	-1.03796125445	2.55977682814	-0.0130151749446	-0.118746243755	-0.0788209023283	0.136520533764	0.00484925881949	-0.142527525474	0.119369704072	0.412349244243	0.0133867738371	0.157526215313	0.0675212580857	-0.0215173025313	0.305264905879	-0.0100871143701	0.142432222953	28.8053928892	-2.76064324097	31.7206422162
7	1.78698357186	-0.210721465969	0.166060879309	0.65353590224	0.107359665911	1.29111911268	-0.107103558349	-0.110080354535	-0.0148140020366	0.130838094465	0.0556272482031	-0.0361793832282	-0.0637507689096	0.12551958124	0.0522253034391	0.185898915217	0.0317421618189	-0.0184991346202	0.156771572874	0.0231001611689	0.115510585743	14.2193576226	2.76483876191	39.342204614
8	6.14968018188	0.816675721219	2.11466094182	1.78834133104	0.142848136735	2.61966243064	-0.0147844513997	0.146606959258	-0.0360388360426	-0.0259685179897	0.0848870769256	0.127042305094	0.0243277756587	-0.0619136027886	-0.0928687137193	0.115200240247	0.0271592063731	0.0045638621871	0.0875994124644	0.00112058397943	0.141526544899	-10.9679712191	-9.90131258263	21.3291155722
9	1.70928966585	0.730952397166	-0.556780502895	1.61147103299	-0.935325465345	1.21907725503	-0.0870949518541	0.4750736115	0.211342617703	-0.212132296221	0.197975418951	0.149441638844	-0.00843587808017	-0.119559322168	-0.109958650539	0.159470699624	-0.0194873633221	-0.0235310110021	0.270231018761	0.0410931735747	0.14613022208	-2.54449615635	0.674667739288	4.80399133492
10	2.18544697002	0.638440001623	-0.760542903119	0.923632178601	-0.850547825157	4.34444303214	0.0284008148818	0.345905215857	0.512501354482	-0.0598560520164	-0.081208589442	0.373539646085	-0.419222813585	0.077576531653	0.0513559378919	0.257484854374	-0.0099634608458	-0.0730620346578	0.244698724967	0.129158074184	0.479159159055	-14.7762787532	14.8691014434	1.55116569941
11	1.54728244959	-0.511254798617	0.782246175738	8.67629641778	-0.754259493492	6.22364017454	-0.0745970129862	0.936024350679	0.262321791335	-0.405754835863	-0.0245965741401	0.387502235223	-0.167018033752	-0.186145069206	0.070029397276	0.187678107957	-0.0333731933936	-0.0592676154939	0.483297769544	0.090458206412	0.245657264524	-12.581075007	2.54707773675	-5.57152927319
12	3.00555575001	0.566189049421	-0.615166552163	0.122708520353	0.110199893369	2.5403204016	-0.0953287213086	0.135646922516	0.361213081037	0.0557252338617	0.0791380152557	0.22151347201	-0.140861690838	-0.142073168629	0.0774153659183	0.137212962742	0.0162277880677	-0.0364223584786	0.219603624256	0.0825890555348	0.260967178778	-18.9902713345	2.30052268472	7.53661296801
13	0.915580424111	-0.0943391317756	-0.936733442061	4.21401606219	4.12900427999	6.81356499808	-0.307250306587	0.358918698114	0.438240477767	-0.0938600545894	-0.1174630903	0.587863932428	-0.223043411791	-0.196559302723	0.405576467048	0.232420852441	0.0491947721644	-0.0951181018387	0.357407869148	0.124633427849	0.404915892496	-25.5981127644	6.37011958291	0.551035728512
14	1.43807954387	-0.0742335482112	0.428886892308	0.611423133531	0.0454465259649	2.56244338777	-0.0653330120973	0.103742054791	0.0855588754031	-0.0523718246091	0.0796893017294	0.188386895357	-0.0875269328993	-0.247118062262	0.00600761962509	0.149106406071	0.0178328730412	-0.0125672577063	0.215730337244	0.0459341892744	0.30453085458	-22.3768043943	-0.462538457902	15.5440911526
15	5.64255038952	1.03950955241	0.966331994844	1.96614784745	0.334975476461	3.44825459917	-0.0536270120817	-0.231435733645	0.122729568882	0.0691668777119	0.0131729716195	0.236661363544	0.0102995959125	-0.311469794172	0.0385967842795	0.111156793948	0.0518014293724	0.03194772807	0.162622837029	0.0252925550929	0.192557296704	-15.8224132444	-3.20510610164	29.8204272563

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 2 through 45 )	A	A	2 - 45	1 - 44
2	2	chain 'A' and (resid 46 through 100 )	A	A	46 - 100	45 - 99
3	3	chain 'A' and (resid 101 through 130 )	A	A	101 - 130	100 - 129
4	4	chain 'A' and (resid 131 through 149 )	A	A	131 - 149	130 - 148
5	5	chain 'A' and (resid 150 through 163 )	A	A	150 - 163	149 - 162
6	6	chain 'A' and (resid 164 through 197 )	A	A	164 - 197	163 - 196
7	7	chain 'A' and (resid 198 through 303 )	A	A	198 - 303	197 - 302
8	8	chain 'B' and (resid 3 through 45 )	B	F	3 - 45	1 - 43
9	9	chain 'B' and (resid 46 through 130 )	B	F	46 - 130	44 - 128
10	10	chain 'B' and (resid 131 through 149 )	B	F	131 - 149	129 - 147
11	11	chain 'B' and (resid 150 through 163 )	B	F	150 - 163	148 - 161
12	12	chain 'B' and (resid 164 through 181 )	B	F	164 - 181	162 - 179
13	13	chain 'B' and (resid 182 through 196 )	B	F	182 - 196	180 - 194
14	14	chain 'B' and (resid 197 through 270 )	B	F	197 - 270	195 - 268
15	15	chain 'B' and (resid 271 through 303 )	B	F	271 - 303	269 - 301

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Movie

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Structure viewers

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Open data

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Validation report

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Assembly

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi