PDB-4gj1: Crystal structure of 1-(5-phosphoribosyl)-5-[(5-phosphoribosylami...

ID or keywords:

Entry

Database: PDB / ID: 4gj1

Title

Crystal structure of 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (hisA).

Components

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Keywords

ISOMERASE / HisA / CSGID / NIAID / Structural Genomics / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / Biosynthesis of secondary metabolites / Histidine metabolism

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 / cytoplasm
Similarity search - Function

Biological species

Campylobacter jejuni subsp. jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.152 Å

Authors

Nocek, B. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Crystal structure of 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (hisA).
Authors: Nocek, B. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Aug 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 22, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.2	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gj1.cif.gz	99.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4gj1.ent.gz	82 KB	Display	PDB format
PDBx/mmJSON format	4gj1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4gj1_validation.pdf.gz	419.2 KB	Display	wwPDB validaton report
Full document	4gj1_full_validation.pdf.gz	421.6 KB	Display
Data in XML	4gj1_validation.xml.gz	10.4 KB	Display
Data in CIF	4gj1_validation.cif.gz	13.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gj/4gj1 ftp://data.pdbj.org/pub/pdb/validation_reports/gj/4gj1	HTTPS FTP

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Related structure data

Similar structure data	1w1a-2 4pa8-d 1ny1-2 5b1d-d 5ac7-2 5xhw-d 5g1t-d 5l6u-d 6rug-d 6nax-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP90547

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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

26.9 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)	35.340, 75.733, 45.923
Angle α, β, γ (deg.)	90.00, 105.18, 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 Mass: 26908.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: jejuni NCTC 11168 = ATCC 700819 / Gene: hisA, Cj1601 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9PM74, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase / Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase

Mass: 26908.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: jejuni NCTC 11168 = ATCC 700819 / Gene: hisA, Cj1601 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9PM74, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.2 Å³/Da / Density % sol: 44.19 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG 3350 , 0.2 M lithium Sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2011 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.15→35 Å / Num. all: 12600 / Num. obs: 12596 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Redundancy: 4.1 % / B_iso Wilson estimate: 52 Å² / R_merge(I) obs: 0.101
Reflection shell	Resolution: 2.15→2.19 Å / % possible all: 98.6

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
Auto-Rickshaw		phasing
PHENIX	(phenix.refine: dev_1117)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.152→34.108 Å / SU ML: 0.29 / σ(F): 2 / σ(I): 0 / Phase error: 25.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.229	1195	4.93 %	RANDOM
R_work	0.1807	-	-	-
all	0.19	-	-	-
obs	0.183	12576	97.15 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.152→34.108 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1714	0	0	43	1757

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	1740
X-RAY DIFFRACTION	f_angle_d	0.861	2344
X-RAY DIFFRACTION	f_dihedral_angle_d	13.315	640
X-RAY DIFFRACTION	f_chiral_restr	0.046	288
X-RAY DIFFRACTION	f_plane_restr	0.002	292

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 (%)
2.1521-2.2383	0.3372	133	0.2724	2196	X-RAY DIFFRACTION	84
2.2383-2.3401	0.2932	136	0.2493	2544	X-RAY DIFFRACTION	97
2.3401-2.4635	0.2838	122	0.2183	2615	X-RAY DIFFRACTION	99
2.4635-2.6178	0.257	150	0.2089	2596	X-RAY DIFFRACTION	99
2.6178-2.8198	0.2594	130	0.2036	2604	X-RAY DIFFRACTION	99
2.8198-3.1034	0.2787	108	0.1985	2681	X-RAY DIFFRACTION	100
3.1034-3.5521	0.2804	151	0.1779	2612	X-RAY DIFFRACTION	100
3.5521-4.4736	0.1826	151	0.1502	2599	X-RAY DIFFRACTION	100
4.4736-34.1118	0.1791	114	0.1621	2589	X-RAY DIFFRACTION	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	7.4198	-3.6839	-1.4256	5.4515	1.4719	2.6299	0.2938	-0.203	0.5528	0.1426	0.0651	-0.9175	0.6047	0.4323	-0.3626	0.333	0.101	-0.0253	0.3648	0.0175	0.3012	6.4675	-0.799	24.5265
2	9.1514	1.134	1.2651	9.1478	-0.7447	2.2866	0.0711	0.4229	0.1832	-1.4004	-0.1704	1.1147	-0.9476	-0.8375	-0.1235	0.4895	0.1431	-0.0937	0.5287	-0.0345	0.4214	-6.3313	11.9373	22.8748
3	1.623	1.4842	1.3888	1.432	0.9333	1.6748	0.5754	0.1104	-0.8704	-0.4154	0.0592	-0.8643	-0.2331	0.4848	-0.279	0.3331	0.0402	0.0111	0.7109	-0.2482	0.7307	-14.4116	1.988	21.1351
4	6.3617	-2.6681	0.4392	3.6767	0.6626	4.6528	0.006	-0.3491	1.0509	0.3787	0.3593	-0.3432	-0.1495	-0.2692	-0.3196	0.3345	-0.0185	-0.0274	0.4042	-0.0589	0.4126	0.7352	10.1668	31.1103
5	2.7076	-1.4015	-0.3738	2.5247	1.309	4.0238	-0.0517	-0.0433	0.227	-0.0837	0.2514	-0.2583	-0.1781	0.2247	-0.1963	0.2645	0.0165	-0.0514	0.397	0.0167	0.346	4.4512	6.8736	22.7775
6	1.7562	-1.5798	0.4035	5.1471	3.6642	4.4549	0.5962	0.8441	1.0373	-0.6808	0.7864	0.5481	-1.7065	-1.6598	-0.2791	0.7471	0.2299	0.0949	0.7978	0.3689	0.6375	-3.8913	16.3236	11.575
7	6.0356	-1.2306	1.6368	3.2093	-2.3311	5.3533	0.4403	-0.6324	0.3854	-0.3112	0.0314	-2.3403	-1.2509	0.7372	-0.2739	0.7752	-0.0961	0.1662	0.3512	-0.1916	0.8143	8.1602	16.6157	22.4937
8	3.2732	-0.4528	-1.3025	4.2862	0.7952	3.2625	0.1259	0.1023	0.5455	-0.8288	-0.1867	-0.3741	-0.6143	-0.5893	-0.1967	0.3941	0.0166	0.0204	0.2755	0.0234	0.3945	5.7613	8.7008	12.931
9	4.533	-0.5542	0.4669	6.5086	-2.2782	7.0334	0.2403	-0.1108	1.0709	-0.5	-0.4257	-0.7798	-0.6583	0.3439	0.0394	0.5054	-0.0538	0.1855	0.3422	0.0427	0.5779	9.4339	11.6277	11.7937
10	0.5641	-0.3854	-0.2001	0.7303	-0.2074	0.3627	0.6798	1.1599	0.5424	-0.5212	0.4356	1.2371	-0.3961	-1.4806	-0.0153	0.497	0.0209	-0.2555	0.8299	0.219	0.6425	-0.4296	2.0238	1.941
11	7.4484	-0.4859	0.7547	7.4599	4.7211	3.5574	0.9409	1.7486	1.4432	-2.0489	-0.5415	-0.4708	-1.2382	-0.0588	0.0159	0.8388	0.0139	0.1979	0.6415	0.0883	0.3722	9.3864	5.1914	-0.4061
12	3.7939	4.2293	-3.404	7.3294	-1.9904	4.2116	-0.546	-0.1536	-1.4843	-0.8472	0.0106	-1.0318	0.4313	0.5517	-0.0174	0.4348	-0.0072	0.0946	0.2603	0.0507	0.4853	9.3263	0.9086	9.0289
13	5.1742	1.7484	2.8525	1.3865	0.0756	3.4893	-0.0198	0.3982	-0.2132	-0.1068	-0.3644	0.364	0.8484	-0.6047	-0.3126	0.6212	-0.2131	-0.1214	0.6091	-0.2256	0.5977	-5.3157	-12.0702	7.0363
14	5.1959	1.6841	-0.2397	7.4149	-0.8834	4.7948	-0.2184	0.9506	-0.7261	-1.4862	0.2154	-0.4571	0.8303	-0.7212	-0.138	0.8323	-0.0852	0.0063	0.6422	-0.0635	0.3454	2.6033	-9.4723	1.3484
15	4.6912	0.7707	-2.921	3.5371	-0.0727	7.4968	0.0047	-0.2638	0.1789	-0.4489	0.2661	-0.8266	0.8169	0.9106	0.039	0.4061	0.0734	0.1245	0.3686	0.0056	0.4704	11.1183	-4.4389	6.5598
16	4.0942	2.5053	1.1816	3.4847	1.3425	6.9369	-1.0355	0.588	-0.971	-0.0729	0.9772	1.5872	1.3747	-0.4142	0.0568	0.7964	-0.0102	0.0874	0.4136	0.113	0.9333	-5.5625	-8.3098	15.0505
17	6.23	0.2559	-0.3972	4.5517	-0.1214	4.4779	0.1323	0.1022	-0.8115	0.0163	-0.2995	0.0181	0.9763	-0.1134	0.0207	0.6631	-0.0201	0.0751	0.3186	-0.0899	0.4517	5.7363	-14.9732	13.3003
18	1.0308	0.3161	-1.1835	1.0536	0.0873	4.5772	-0.1217	-0.2492	-0.1815	0.6129	0.1624	0.2287	1.1213	-0.3503	0.1229	0.6027	-0.009	0.1055	0.348	0.0104	0.3681	2.09	-8.6615	23.2508
19	2.4629	-1.1309	-0.996	6.4997	3.1354	4.2661	-0.267	0.1102	-0.3183	0.8221	-0.0827	0.4234	0.7439	-0.2395	0.3652	0.4635	-0.0031	0.0021	0.3907	0.0027	0.3227	2.3297	-6.3683	25.7881
20	0.7326	0.2624	-1.0018	1.3171	0.8376	2.6192	-0.813	-1.0685	-0.2106	1.1344	0.9676	-0.7566	1.1942	0.6876	0.0819	0.8511	0.33	-0.0775	0.7192	-0.0063	0.3931	7.8866	-6.086	33.2456

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:8)
2	X-RAY DIFFRACTION	2	(chain A and resid 9:16)
3	X-RAY DIFFRACTION	3	(chain A and resid 17:28)
4	X-RAY DIFFRACTION	4	(chain A and resid 29:40)
5	X-RAY DIFFRACTION	5	(chain A and resid 41:56)
6	X-RAY DIFFRACTION	6	(chain A and resid 57:64)
7	X-RAY DIFFRACTION	7	(chain A and resid 65:75)
8	X-RAY DIFFRACTION	8	(chain A and resid 76:88)
9	X-RAY DIFFRACTION	9	(chain A and resid 89:102)
10	X-RAY DIFFRACTION	10	(chain A and resid 103:109)
11	X-RAY DIFFRACTION	11	(chain A and resid 110:121)
12	X-RAY DIFFRACTION	12	(chain A and resid 122:130)
13	X-RAY DIFFRACTION	13	(chain A and resid 131:141)
14	X-RAY DIFFRACTION	14	(chain A and resid 142:160)
15	X-RAY DIFFRACTION	15	(chain A and resid 161:169)
16	X-RAY DIFFRACTION	16	(chain A and resid 170:175)
17	X-RAY DIFFRACTION	17	(chain A and resid 181:197)
18	X-RAY DIFFRACTION	18	(chain A and resid 198:211)
19	X-RAY DIFFRACTION	19	(chain A and resid 212:231)
20	X-RAY DIFFRACTION	20	(chain A and resid 232:243)

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