PDB-2w79: Establishing wild-type levels of catalytic activity on natural an...

ID or keywords:

Entry

Database: PDB / ID: 2w79

Title

Establishing wild-type levels of catalytic activity on natural and artificial (ba)8-barrel protein scaffolds

Components

1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE

Keywords

ISOMERASE / HISTIDINE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS

Function / homology

Function and homology information

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / L-histidine biosynthetic process / tryptophan biosynthetic process /

cytoplasm
Similarity search - Function

Biological species

THERMOTOGA MARITIMA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Claren, J. / Malisi, C. / Hocker, B. / Sterner, R.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Establishing Wild-Type Levels of Catalytic Activity on Natural and Artificial (Beta Alpha)8- Barrel Protein Scaffolds.
Authors: Claren, J. / Malisi, C. / Hocker, B. / Sterner, R.

History

Deposition	Dec 21, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 17, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2w79.cif.gz	115 KB	Display	PDBx/mmCIF format
PDB format	pdb2w79.ent.gz	90.3 KB	Display	PDB format
PDBx/mmJSON format	2w79.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/w7/2w79 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/2w79	HTTPS FTP

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Related structure data

Related structure data	1qo2S 2cff S: Starting model for refinement
Similar structure data	1qo2-1 5ocj-1 2cff-1 5ab3-1 5ac7-1 1h5y-1 2cff-2 2feo-d 3k60-2 2bkv-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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE

B: 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE

hetero molecules

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

1

A: 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE

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

2

B: 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.000, 64.100, 79.200
Angle α, β, γ (deg.)	90.00, 94.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE / PHOSPHORIBOSYLFORMIMINO-5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMERASE / N-PHOSPHORIBOSYL- ...PHOSPHORIBOSYLFORMIMINO-5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMERASE / N-PHOSPHORIBOSYL-FORMIMINO-AMINOIMIDAZOL-CARBOXAMID RIBONUCLEOTID ISOMERASE Mass: 27001.283 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET21A-HISA-II / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): T7-EXPRESS References: UniProt: Q9X0C7, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, HIS 75 TO TYR ENGINEERED RESIDUE IN CHAIN A, PHE 111 TO SER ...ENGINEERED RESIDUE IN CHAIN A, HIS 75 TO TYR ENGINEERED RESIDUE IN CHAIN A, PHE 111 TO SER ENGINEERED RESIDUE IN CHAIN A, ASP 127 TO VAL ENGINEERED RESIDUE IN CHAIN A, ASP 169 TO VAL ENGINEERED RESIDUE IN CHAIN B, HIS 75 TO TYR ENGINEERED RESIDUE IN CHAIN B, PHE 111 TO SER ENGINEERED RESIDUE IN CHAIN B, ASP 127 TO VAL ENGINEERED RESIDUE IN CHAIN B, ASP 169 TO VAL

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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: 41.5 % / Description: NONE
Crystal grow	pH: 7.5 / Details: 0.1 M TRIS-HCL PH 7.5, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.992
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.992 Å / Relative weight: 1
Reflection	Resolution: 1.85→40 Å / Num. obs: 42406 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / R_merge(I) obs: 0.05 / Net I/σ(I): 13.4
Reflection shell	Resolution: 1.85→1.96 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 2.5 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
REFMAC	5.4.0066	refinement
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QO2

1qo2

Resolution: 1.85→33.63 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.927 / SU B: 10.613 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.267	2082	5 %	RANDOM
R_work	0.202	-	-	-
obs	0.206	39541	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 26.07 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	-0.01 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	0 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→33.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3764	0	1	378	4143

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	3859
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.319	1.993	5201
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.061	5	491
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.662	24.074	162
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.008	15	763
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.289	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	612
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2785
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.053	2	2392
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.703	3	3869
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.18	2	1467
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.869	3	1325
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.85→1.9 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.372	152	-
R_work	0.334	2885	-
obs	-	-	100 %

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	0.3377	0.9973	-0.2923	4.8569	0.3732	1.0526	-0.1552	-0.1058	-0.0351	-0.0875	0.271	-0.2693	-0.3201	0.2571	-0.1159	0.0731	-0.0679	0.06	0.1182	-0.0457	0.0768	22.053	7.113	36.035
2	0.5173	0.8408	-0.8602	2.6229	-0.3012	5.0908	-0.028	-0.0507	-0.0041	0.037	0.1101	-0.1819	0.0638	0.315	-0.0821	0.0202	0.0142	0.0341	0.0655	-0.0256	0.0804	21.891	-2.185	36.86
3	3.6316	0.6131	1.0426	0.44	-0.2557	3.2775	-0.2435	0.2704	-0.257	0.0549	0.1814	0.1471	0.3467	0.1834	0.0621	0.0706	0.005	0.0459	0.0184	-0.0331	0.1055	14.627	-8.329	31.045
4	1.9657	-1.6469	0.3885	5.8276	-0.2308	1.3676	0.0303	-0.0022	-0.0786	0.1473	0.0646	0.4043	0.1477	-0.1616	-0.095	-0.0173	-0.0327	0.0441	-0.0048	-0.0113	0.165	3.887	-5.804	30.951
5	5.9885	3.2233	2.2196	2.6183	5.8126	24.9624	-0.9271	-0.0114	0.4686	-0.4514	0.5345	0.5082	-1.2403	-0.7501	0.3926	0.0465	0.0748	-0.0966	-0.0142	0.0625	0.3197	-3.016	7.708	24.862
6	0.8904	0.3134	0.595	0.1483	-0.0738	2.5106	0.1043	-0.2175	0.3362	0.2634	-0.0149	0.3093	0.0101	-0.2907	-0.0893	-0.0553	0.0062	0.0811	0.0481	-0.01	0.2658	0.382	3.521	35.445
7	1.7883	1.0519	0.691	1.4389	0.1835	2.1287	0.2002	-0.161	0.2686	0.4928	-0.1148	0.2896	-0.0095	-0.3108	-0.0853	0.0744	-0.0222	0.2108	0.0772	-0.0657	0.1692	3.378	4.714	47.333
8	11.3136	3.7956	-0.5251	10.4931	-5.4147	5.7547	0.1588	-0.9834	0.0647	0.894	0.0956	-0.4669	0.3668	-0.0362	-0.2544	0.3864	-0.0579	0.0587	0.1787	-0.1136	-0.0616	17.326	4.329	53.559
9	1.8648	0.57	-0.4087	1.5387	1.1462	1.2738	0.1121	-0.0494	0.1909	-0.0028	0.0007	0.127	0.0686	0.1469	-0.1129	0.0246	-0.0145	0.0789	0.0771	-0.003	0.0634	17.233	36.805	76.05
10	1.251	1.9901	-0.733	9.5103	-2.1038	6.6869	0.0645	-0.0596	-0.18	0.7914	0.139	-1.0549	-0.0348	0.2871	-0.2034	0.0212	0.0379	-0.0934	0.0033	-0.044	0.0916	22.931	32.322	80.853
11	0.2041	-0.1734	-0.0986	1.7829	-0.1797	1.992	0.1311	0.0078	-0.009	0.0513	0.0676	0.0404	0.0205	0.1046	-0.1988	0.055	0.0112	0.0309	0.0375	-0.0169	0.0728	18.376	26.33	72.968
12	1.5589	-0.2845	0.6829	1.5559	-0.2396	0.7457	0.1322	0.0172	-0.0709	-0.0237	-0.0655	0.3056	0.134	-0.0006	-0.0668	0.0342	0.0112	-0.012	0.0112	-0.0402	0.1445	6.512	24.077	67.414
13	1.1458	0.1061	-3.9094	6.1121	-5.1977	17.171	-0.7013	0.2498	1.2881	-0.661	0.4055	1.0449	-0.1553	-0.9717	0.2959	0.0362	0.0194	-0.1512	0.0957	-0.0929	0.5122	-3.367	40.179	65.048
14	1.6714	2.3622	1.8935	3.6758	2.2175	2.7691	-0.0141	-0.225	0.027	-0.0777	-0.2378	0.5465	-0.0697	-0.2874	0.252	-0.0472	0.004	0.0587	0.0818	-0.0933	0.2609	-0.725	35.51	75.409
15	2.9117	0.3371	1.1196	1.8304	0.6826	2.3221	-0.0384	-0.1738	0.1509	0.4352	-0.2773	0.7695	0.1388	-0.3291	0.3158	0.033	-0.033	0.2193	0.1072	-0.1005	0.2399	-1.197	36.108	84.303
16	1.5479	-0.1774	0.7247	1.1935	1.4655	2.3832	-0.058	-0.0913	-0.1122	0.5335	-0.144	0.2004	0.2251	-0.2882	0.2021	0.1584	-0.0878	0.166	0.0879	-0.026	0.0862	7.3	33.942	89.603

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 33
2	X-RAY DIFFRACTION	2	A	34 - 66
3	X-RAY DIFFRACTION	3	A	67 - 108
4	X-RAY DIFFRACTION	4	A	109 - 131
5	X-RAY DIFFRACTION	5	A	132 - 143
6	X-RAY DIFFRACTION	6	A	144 - 173
7	X-RAY DIFFRACTION	7	A	174 - 226
8	X-RAY DIFFRACTION	8	A	227 - 241
9	X-RAY DIFFRACTION	9	B	1 - 21
10	X-RAY DIFFRACTION	10	B	22 - 44
11	X-RAY DIFFRACTION	11	B	45 - 77
12	X-RAY DIFFRACTION	12	B	78 - 130
13	X-RAY DIFFRACTION	13	B	131 - 147
14	X-RAY DIFFRACTION	14	B	148 - 177
15	X-RAY DIFFRACTION	15	B	178 - 206
16	X-RAY DIFFRACTION	16	B	207 - 241

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