PDB-5lhf: Phosphoribosyl anthranilate isomerase from Thermococcus kodakaraensis

ID or keywords:

Entry

Database: PDB / ID: 5lhf

Title

Phosphoribosyl anthranilate isomerase from Thermococcus kodakaraensis

Components

N-(5'-phosphoribosyl)anthranilate isomerase

Keywords

ISOMERASE /

tryptophan biosynthesis /

TIM barrel /

protein stability

Function / homology

Function and homology information

phosphoribosylanthranilate isomerase /

phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function

Biological species

Thermococcus kodakarensis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.75 Å

Authors

Perveen, S. / Rashid, N. / Papageorgiou, A.C.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of a phosphoribosyl anthranilate isomerase from the hyperthermophilic archaeon Thermococcus kodakaraensis.
Authors: Perveen, S. / Rashid, N. / Papageorgiou, A.C.

History

Deposition	Jul 11, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Dec 21, 2016	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5lhf.cif.gz	189.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5lhf.ent.gz	151.2 KB	Display	PDB format
PDBx/mmJSON format	5lhf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	5lheSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5lhe-d 3wjx-d 7a8s-d 4n2y-6 5nlc-1 5nlc-2 3sgu-d 4kdu-1 3nq2-2 4n2y-3 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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: N-(5'-phosphoribosyl)anthranilate isomerase

B: N-(5'-phosphoribosyl)anthranilate isomerase

hetero molecules

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

1

A: N-(5'-phosphoribosyl)anthranilate isomerase

hetero molecules

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

2

B: N-(5'-phosphoribosyl)anthranilate isomerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	29.678, 47.144, 88.518
Angle α, β, γ (deg.)	102.61, 93.88, 108.34
Int Tables number	1
Space group name H-M	P1

#1: Protein	N-(5'-phosphoribosyl)anthranilate isomerase / PRAI Mass: 23217.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HYPERTHERMOPHILE Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Gene: trpF, TK0256 / Plasmid: TKTrpF-pET28a / Details (production host): E.coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus RIL References: UniProt: Q9YGB1, phosphoribosylanthranilate isomerase
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.3 Å³/Da / Density % sol: 47 % / Description: Rods
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris-HCl (pH 8.0), 0.2 M sodium formate, 13% (w/v) PEG 4000.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: MASSIF-1 / Wavelength: 0.96598 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 10, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.96598 Å / Relative weight: 1

Reflection

Resolution: 1.75→43.28 Å / Num. obs: 40054 / % possible obs: 90.4 % / Redundancy: 1.8 % / B_iso Wilson estimate: 11.7 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.047 / Net I/σ(I): 8.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	Diffraction-ID	% possible all
1.75-1.78	1.6	0.494	0.76	1	77.8
8.62-43.28	2	0.021	0.998	1	93.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
Aimless	0.5.15	data scaling
PHASER		phasing
PDB_EXTRACT	3.2	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5LHE

5lhe

Resolution: 1.75→43.294 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2143	2008	5.01 %
R_work	0.1726	-	-
obs	0.1747	40050	90.42 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.75→43.294 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3242	0	4	622	3868

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3324
X-RAY DIFFRACTION	f_angle_d	0.82	4500
X-RAY DIFFRACTION	f_dihedral_angle_d	17.488	2058
X-RAY DIFFRACTION	f_chiral_restr	0.055	517
X-RAY DIFFRACTION	f_plane_restr	0.005	579

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 (%)
1.75-1.7938	0.3495	129	0.2689	2305	X-RAY DIFFRACTION	79
1.7938-1.8423	0.3286	153	0.2383	2566	X-RAY DIFFRACTION	84
1.8423-1.8965	0.2722	144	0.2253	2645	X-RAY DIFFRACTION	89
1.8965-1.9577	0.2939	139	0.2183	2767	X-RAY DIFFRACTION	90
1.9577-2.0277	0.2232	120	0.1968	2771	X-RAY DIFFRACTION	93
2.0277-2.1089	0.2465	116	0.1814	2789	X-RAY DIFFRACTION	91
2.1089-2.2048	0.2055	147	0.1794	2755	X-RAY DIFFRACTION	93
2.2048-2.3211	0.2124	147	0.1791	2786	X-RAY DIFFRACTION	92
2.3211-2.4665	0.2518	151	0.1757	2795	X-RAY DIFFRACTION	92
2.4665-2.6569	0.2075	148	0.1778	2756	X-RAY DIFFRACTION	93
2.6569-2.9242	0.22	150	0.1745	2759	X-RAY DIFFRACTION	92
2.9242-3.3472	0.1755	142	0.1607	2781	X-RAY DIFFRACTION	92
3.3472-4.2166	0.1879	152	0.1361	2786	X-RAY DIFFRACTION	93
4.2166-43.3073	0.1796	170	0.1533	2781	X-RAY DIFFRACTION	94

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	0.1201	0.0643	-0.0111	0.1657	-0.1036	0.2242	0.0589	-0.0657	-0.0549	0.0662	0.0385	0.002	-0.0697	-0.0211	0.1083	0.0755	-0.0103	0.0018	0.0738	-0.0079	0.0866	-15.3522	-99.2038	-8.5782
2	0.0845	0.138	-0.0068	0.2983	-0.1219	0.3071	0.1012	-0.0707	0.0049	0.1128	-0.0109	0.0209	-0.038	0.0064	0.1844	0.1865	-0.0873	0.0135	0.1213	0.0118	0.0677	-16.2002	-108.2782	0.5455
3	0.0833	0.0052	0.0481	0.0915	0.0076	0.0749	0.0504	-0.0422	-0.0199	0.1395	0.0468	0.0468	0.0366	-0.0859	0.0825	0.0829	-0.0156	0.029	0.0826	-0.0037	0.0993	-20.0566	-112.1411	-7.4741
4	0.0604	-0.1145	0.0922	0.2248	-0.1776	0.1412	0.0476	-0.0185	-0.0058	-0.1574	0.1086	0.291	0.0769	0.0014	0.0791	0.0868	-0.0601	-0.0443	0.1135	0.014	0.2208	-25.0699	-114.6921	-15.0408
5	0.0079	-0.0032	0.0075	0.0099	0.0026	0.0172	0.0565	0.0564	-0.042	-0.0348	0.0251	-0.0285	0.0368	0.0393	0.0412	0.3459	0.0029	0.004	0.1874	-0.0362	0.0946	-13.9742	-108.4509	-29.7238
6	0.05	-0.0257	0.0272	0.053	0.0419	0.1591	0.0666	0.0465	-0.0785	-0.1564	0.0475	0.0521	0.1729	0.0637	0.3691	0.3311	-0.0488	-0.1457	0.1546	-0.0255	0.0517	-20.6693	-107.9434	-30.3959
7	0.045	-0.0424	-0.0312	0.0698	0.0673	0.0696	0.013	-0.0109	0.0062	0.0038	-0.0092	-0.0138	-0.0159	0.032	-0.0059	0.2865	0.015	0.0007	0.2289	-0.003	0.0634	-10.3221	-98.8793	-32.2351
8	0.0326	-0.0454	-0.0236	0.1026	0.0329	0.0158	0.0476	0.0055	0.0376	-0.2582	0.0263	0.0225	-0.0368	-0.0502	0.112	0.1378	-0.0291	-0.0216	0.1366	0.0131	0.0863	-17.8502	-95.1192	-25.9878
9	0.0039	-0.001	0.0048	0.008	-0.0104	0.0218	-0.0003	0.0463	-0.0225	0.017	0.0239	-0.0356	-0.0187	0.0288	0.0015	0.0794	-0.013	-0.0046	0.1154	-0.0043	0.1195	-8.4204	-91.0249	-10.1091
10	0.0013	-0.0009	-0.0006	0.0007	0.0015	0.0074	-0.0344	-0.0065	0.0074	-0.0254	0.0331	0.0215	-0.0459	-0.0223	-0.0002	0.176	-0.0209	-0.0127	0.162	0.0168	0.1446	-18.3147	-84.9104	-17.4855
11	0.0016	0.0044	-0.0049	0.0173	-0.0213	0.0275	-0.0141	0.0036	-0.0382	0.0365	-0.009	0.0287	0.0569	-0.0321	0.0034	0.11	0.0124	0.0372	0.1518	0.0236	0.1877	-39.2774	-132.9779	22.5831
12	0.0021	-0.0029	-0.0043	0.0131	-0.0038	0.0183	0.0824	0.0078	-0.0307	-0.0696	0.0652	0.0177	-0.0632	0.0085	0.0003	0.1491	0.0129	-0.0071	0.0885	-0.0126	0.0778	-28.0972	-124.8985	7.1879
13	0.1108	-0.0007	-0.0213	0.3028	-0.0686	0.194	0.1296	0.117	0.0472	-0.1421	-0.0321	-0.0411	-0.0019	-0.0802	0.0787	0.0695	0.0111	0.0039	0.078	-0.0104	0.1	-28.7956	-121.5504	7.846
14	0.0352	0.0054	-0.003	0.0183	0.0164	0.0322	0.0275	0.0169	0.0201	-0.0957	0.0058	0.0686	0.0206	-0.051	-0.0014	0.1167	0.0196	-0.0537	0.0867	-0.0267	0.1049	-34.5871	-119.1276	6.7113
15	0.0601	0.086	-0.1089	0.1385	-0.1654	0.2041	0.0474	-0.0089	0.0217	0.0563	0.0933	0.2742	-0.046	-0.0291	0.1968	0.0393	0.0629	0.0285	0.0566	0.0406	0.2375	-38.17	-108.4394	14.5177
16	0.0874	0.0936	-0.045	0.1006	-0.0484	0.0232	0.0375	-0.0524	0.0152	0.0222	0.0778	-0.0178	-0.0476	0.0111	0.0153	0.2745	0.0237	-0.0311	0.202	-0.0217	0.0985	-28.7783	-115.7121	30.669
17	0.149	0.095	0.0182	0.213	0.0713	0.0241	0.0989	-0.1041	0.1455	0.2041	0.1118	0.0367	-0.1616	0.0692	0.3489	0.2842	0.0983	0.1198	0.2093	-0.0217	0.1042	-35.069	-116.269	32.6008
18	0.0632	-0.0066	0.054	0.2284	0.0604	0.0671	0.0053	-0.0786	-0.0374	0.2587	0.0905	0.1224	0.035	0.0346	0.0456	0.1887	0.0311	0.0275	0.1473	-0.0007	0.1052	-29.388	-127.0419	30.4623
19	0.0937	-0.0963	-0.028	0.1565	-0.0127	0.0639	0.05	-0.0171	-0.0411	0.0652	0.0749	0.0436	-0.0164	-0.0022	0.2464	0.0344	0.0553	0.0524	0.1209	0.0009	0.0691	-26.6878	-132.0945	17.8376
20	0.0172	0.0028	0.0111	0.0173	0.0034	0.012	0.0236	0.0167	0.0031	0.0331	0.0813	0.0402	0.0432	-0.0252	0.0018	0.1046	0.0182	-0.0147	0.0847	-0.0077	0.1457	-32.0165	-138.7945	19.0529

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:37)
2	X-RAY DIFFRACTION	2	(chain A and resid 38:48)
3	X-RAY DIFFRACTION	3	(chain A and resid 49:75)
4	X-RAY DIFFRACTION	4	(chain A and resid 76:101)
5	X-RAY DIFFRACTION	5	(chain A and resid 102:110)
6	X-RAY DIFFRACTION	6	(chain A and resid 111:136)
7	X-RAY DIFFRACTION	7	(chain A and resid 137:149)
8	X-RAY DIFFRACTION	8	(chain A and resid 150:183)
9	X-RAY DIFFRACTION	9	(chain A and resid 184:201)
10	X-RAY DIFFRACTION	10	(chain A and resid 202:208)
11	X-RAY DIFFRACTION	11	(chain B and resid 0:5)
12	X-RAY DIFFRACTION	12	(chain B and resid 6:14)
13	X-RAY DIFFRACTION	13	(chain B and resid 15:44)
14	X-RAY DIFFRACTION	14	(chain B and resid 45:60)
15	X-RAY DIFFRACTION	15	(chain B and resid 61:101)
16	X-RAY DIFFRACTION	16	(chain B and resid 102:109)
17	X-RAY DIFFRACTION	17	(chain B and resid 110:136)
18	X-RAY DIFFRACTION	18	(chain B and resid 137:172)
19	X-RAY DIFFRACTION	19	(chain B and resid 173:199)
20	X-RAY DIFFRACTION	20	(chain B and resid 200:208)

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