PDB-3nz1: Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed w...

ID or keywords:

Entry

Database: PDB / ID: 3nz1

Title

Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole

Components

Indole-3-glycerol phosphate synthase

Keywords

LYASE / Tim Barrel / Kemp Elimination Enzyme

Function / homology

Function and homology information

indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / L-tryptophan biosynthetic process
Similarity search - Function

Biological species

Sulfolobus solfataricus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.56 Å

Authors

Lee, T.M. / Privett, H.K. / Kaiser, J.T. / Mayo, S.L.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Iterative approach to computational enzyme design.
Authors: Privett, H.K. / Kiss, G. / Lee, T.M. / Blomberg, R. / Chica, R.A. / Thomas, L.M. / Hilvert, D. / Houk, K.N. / Mayo, S.L.

History

Deposition	Jul 15, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 29, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Apr 25, 2012	Group: Database references
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3nz1.cif.gz	73.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3nz1.ent.gz	56 KB	Display	PDB format
PDBx/mmJSON format	3nz1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3nz1_validation.pdf.gz	470.3 KB	Display	wwPDB validaton report
Full document	3nz1_full_validation.pdf.gz	477.8 KB	Display
Data in XML	3nz1_validation.xml.gz	15.5 KB	Display
Data in CIF	3nz1_validation.cif.gz	21.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nz/3nz1 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/3nz1	HTTPS FTP

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Related structure data

Related structure data	3nydC 3nyzC 3o2lC C: citing same article (ref.)
Similar structure data	3q40-d 4iww-2 3rod-3 6k2t-d 3c6y-d 2pkc-d 2id8-d 6clb-d 1lbl-d 4wxs-d 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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (2)

Deposited unit

A: Indole-3-glycerol phosphate synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	60.720, 60.720, 120.180
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Indole-3-glycerol phosphate synthase / IGPS Mass: 30010.518 Da / Num. of mol.: 1 Mutation: E51A, S81A, L83A, K110W, L131A, L157A, E159V, G178E, N180A, E210W, S211Q, L231G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, trpC / Production host: Escherichia coli (E. coli) References: UniProt: Q06121, indole-3-glycerol-phosphate synthase
#2: Chemical	ChemComp-3NY / 5-nitro-1H-benzotriazole Mass: 164.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₄N₄O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₆O₆
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.28 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 potassium sodium tartrate, 2M ammonium sulfate, 0.1 M sodium citrate/citric acid, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 1.013 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2009 / Details: Flat mirror

Radiation

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

Radiation wavelength

Wavelength: 1.013 Å / Relative weight: 1

Reflection

Resolution: 1.56→52.585 Å / Num. all: 37246 / Num. obs: 37246 / % possible obs: 99.8 % / Redundancy: 4 % / R_sym value: 0.066 / Net I/σ(I): 8.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.56-1.64	4	0.504	1.2	21420	5386	0.504	100
1.64-1.74	4	0.331	2.1	20262	5063	0.331	100
1.74-1.86	4	0.229	1.5	19087	4774	0.229	100
1.86-2.01	4	0.141	2.2	17990	4473	0.141	99.9
2.01-2.21	4	0.085	6.6	16631	4125	0.085	99.8
2.21-2.47	4	0.067	8.6	15104	3738	0.067	99.8
2.47-2.85	4	0.058	9.8	13484	3335	0.058	99.9
2.85-3.49	4	0.055	6.6	11421	2848	0.055	100
3.49-4.93	4	0.056	9.2	8867	2239	0.056	99.8
4.93-40.06	3.7	0.04	13.3	4722	1265	0.04	95.8

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 44.26 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	40.06 Å
Translation	2.5 Å	40.06 Å

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Processing

Software

Name	Version	Classification
SCALA	3.3.12	data scaling
PHASER	2.1.4	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
Blu-Ice		data collection
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.56→52.58 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.959 / WR_factor R_free: 0.2228 / WR_factor R_work: 0.1842 / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8659 / SU B: 3.752 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0823 / SU R_free: 0.0861 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2104	1856	5 %	RANDOM
R_work	0.1723	-	-	-
obs	0.1742	37189	99.7 %	-
all	-	37246	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 61.94 Å² / B_iso mean: 13.5747 Å² / B_iso min: 2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.58 Å²	0.29 Å²	-0 Å²
2-	-	0.58 Å²	-0 Å²
3-	-	-	-0.86 Å²

Refinement step

Cycle: LAST / Resolution: 1.56→52.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2007	0	72	181	2260

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.027	0.022	2190
X-RAY DIFFRACTION	r_angle_refined_deg	2.397	2.002	2969
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.135	5	267
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.176	23.465	101
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.295	15	410
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.823	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.198	0.2	327
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.021	1643
X-RAY DIFFRACTION	r_mcbond_it	1.354	1.5	1299
X-RAY DIFFRACTION	r_mcangle_it	2.113	2	2116
X-RAY DIFFRACTION	r_scbond_it	3.38	3	891
X-RAY DIFFRACTION	r_scangle_it	5.32	4.5	852

LS refinement shell

Resolution: 1.56→1.601 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.329	134	-
R_work	0.298	2579	-
all	-	2713	-
obs	-	-	99.89 %

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	1.6757	1.2218	0.0337	5.7755	1.1444	3.0242	-0.028	0.1952	-0.1035	-0.2491	0.031	0.0383	0.0483	-0.0897	-0.0031	0.1052	0.011	-0.0041	0.1294	0.0073	0.12	36.472	-17.1978	-3.9497
2	2.8141	2.3116	0.7589	8.442	-8.1957	12.8058	0.0101	0.2587	-0.2181	-0.2483	-0.1739	-0.6006	0.3818	0.7622	0.1638	0.0954	0.0083	-0	0.1333	-0.0618	0.2137	41.3529	-19.1849	3.9798
3	3.4614	-1.4915	-0.1418	1.5358	-0.3576	0.3628	-0.1178	-0.3951	-0.2299	0.2214	0.0554	0.141	0.0539	0.0502	0.0624	0.1664	-0.0148	0.0101	0.1099	-0.0157	0.1333	32.9903	-22.038	22.2391
4	2.0082	-3.2947	5.1026	6.3749	-9.4688	14.6061	0.022	-0.2533	-0.2079	0.1396	0.1094	-0.0127	0.1183	-0.177	-0.1314	0.2148	-0.0056	-0.0389	0.219	0.0747	0.222	17.5001	-16.5083	19.4034
5	7.6991	-0.9781	0.0744	2.958	1.2456	7.0776	-0.0134	-0.0323	-0.1057	0.0704	-0.0144	0.2803	0.0629	-0.2659	0.0279	0.0905	-0.0153	0.0041	0.0894	0.0066	0.0889	8.8131	-8.1646	17.108
6	0.5837	0.386	0.1015	0.4087	-0.0067	0.4674	0.01	-0.0083	0.0219	-0.0049	-0.0007	-0.0662	-0.0079	0.0755	-0.0093	0.1004	0.0037	-0.001	0.0869	0.0008	0.0935	30.8162	-1.7638	13.0948
7	9.3208	-1.1117	-0.7825	2.6909	0.007	3.5677	-0.0184	-0.429	-0.0887	0.3169	-0.0107	-0.0871	0.0254	0.0272	0.0292	0.1283	-0.0037	-0.001	0.0961	-0.0049	0.1074	27.6197	-1.8141	24.4616
8	8.5011	-4.4063	-2.9098	10.0231	-4.404	5.7363	0.019	-0.8941	0.784	0.9287	0.1577	-0.6553	-0.6836	0.4019	-0.1767	0.1492	-0.0416	-0.0107	0.2074	0.0154	0.1679	18.6279	-1.2293	22.6729
9	4.95	0.496	-2.7056	1.6506	-0.3183	4.2901	0.0244	-0.0905	0.0652	-0.0266	0.0034	-0.168	0.0039	0.2313	-0.0278	0.1059	-0.0031	-0.0139	0.078	-0.0026	0.0954	36.238	-9.7244	11.9002
10	1.581	-0.4436	-0.6026	1.0356	0.69	1.21	-0.0013	-0.0881	0.0574	0.064	0.0126	-0.0222	-0.0444	0.0229	-0.0114	0.1036	-0.0056	-0.0019	0.0848	0.0106	0.1059	30.0899	-13.1476	18.8814
11	0.9043	-0.3509	0.0823	0.5482	-0.209	2.6001	-0.014	-0.0449	-0.1478	0.0286	0.0133	0.0168	0.1767	0.0436	0.0006	0.0922	-0.0113	-0.0005	0.0872	-0.0017	0.1062	28.8136	-21.194	13.858
12	2.5703	0.6935	-1.1219	1.2684	-0.1735	3.6984	-0.0244	0.105	-0.0349	-0.0685	0.0216	-0.0234	0.1198	0.0261	0.0029	0.074	0.0126	-0.0097	0.0695	-0.0064	0.0959	25.2638	-25.1091	4.9852
13	1.9212	0.7333	-0.9472	2.8968	-1.8762	5.9635	-0.0058	0.1148	0.0111	-0.1274	-0.0095	-0.0098	0.0077	0.0624	0.0152	0.0678	0.0134	-0.0021	0.0826	-0.013	0.1164	21.9006	-15.2257	0.0311
14	1.0533	-0.2265	0.1572	2.8224	0.9907	3.0245	-0.0211	-0.0243	-0.1337	0.0754	0.0153	0.0481	0.1848	-0.091	0.0057	0.0725	0.006	-0.0061	0.0979	0.0042	0.0987	17.4215	-17.7335	1.3912
15	9.7574	0.0033	0.6749	2.1307	-0.3557	3.2505	0.0548	0.2105	-0.0554	-0.1328	-0.0386	-0.0652	0.081	0.1001	-0.0162	0.1309	-0.0099	0.004	0.0758	-0.0002	0.0817	24.3614	-3.6462	-4.1787
16	0.9621	-0.4761	0.3279	1.586	-0.7574	6.6316	-0.046	0.0839	-0.1089	-0.1031	0.0832	0.3646	0.2951	-0.4654	-0.0372	0.0989	0.0103	0.0005	0.0978	-0.0035	0.1173	11.9628	-11.5528	0.91
17	1.7684	-0.9577	-0.5964	4.396	1.2231	0.8789	-0.007	-0.0509	0.2225	0.022	0.0329	-0.1026	-0.1451	-0.0464	-0.0258	0.1216	-0.0053	-0.0039	0.1306	0.004	0.1018	19.2739	2.3462	6.104
18	6.3948	4.688	2.3226	8.8405	1.353	5.8492	-0.0852	0.2348	0.3854	-0.2683	0.0614	0.2974	-0.4022	-0.1868	0.0238	0.125	0.0207	0.0056	0.1335	0.003	0.1286	11.2431	1.0436	4.1448
19	3.159	1.5424	1.1791	1.3463	0.7347	1.1964	-0.0792	-0.0182	0.2398	-0.0456	0.0048	0.0789	-0.1392	0.0404	0.0745	0.0953	0.0084	0.0039	0.086	0.0046	0.0874	23.301	0.7034	11.8085
20	9.4176	1.1594	2.6452	2.6667	2.526	2.999	-0.0174	0.0229	0.5422	-0.1153	-0.0464	0.0795	-0.3786	-0.0877	0.0638	0.2445	0.0254	0.05	0.1076	0.0188	0.1314	18.4135	6.493	16.4534

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 9
2	X-RAY DIFFRACTION	2	A	10 - 18
3	X-RAY DIFFRACTION	3	A	19 - 28
4	X-RAY DIFFRACTION	4	A	29 - 34
5	X-RAY DIFFRACTION	5	A	35 - 44
6	X-RAY DIFFRACTION	6	A	45 - 64
7	X-RAY DIFFRACTION	7	A	65 - 74
8	X-RAY DIFFRACTION	8	A	75 - 79
9	X-RAY DIFFRACTION	9	A	80 - 91
10	X-RAY DIFFRACTION	10	A	92 - 114
11	X-RAY DIFFRACTION	11	A	115 - 134
12	X-RAY DIFFRACTION	12	A	135 - 153
13	X-RAY DIFFRACTION	13	A	154 - 165
14	X-RAY DIFFRACTION	14	A	166 - 180
15	X-RAY DIFFRACTION	15	A	181 - 196
16	X-RAY DIFFRACTION	16	A	197 - 208
17	X-RAY DIFFRACTION	17	A	209 - 217
18	X-RAY DIFFRACTION	18	A	218 - 226
19	X-RAY DIFFRACTION	19	A	227 - 240
20	X-RAY DIFFRACTION	20	A	241 - 248

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