PDB-4esx: Crystal structure of C. albicans Thi5 complexed with PLP

ID or keywords:

Entry

Database: PDB / ID: 4esx

Title

Crystal structure of C. albicans Thi5 complexed with PLP

Components

Pyrimidine biosynthesis enzyme THI13

Keywords

TRANSFERASE / Thiamin pyrimidine biosynthesis

Function / homology

Function and homology information

4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity from histidine and PLP / Transferases / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / metal ion binding
Similarity search - Function

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.2 Å

Authors

Huang, S. / Fenwick, M.K. / Zhang, Y. / Lai, R. / Hazra, A. / Rajashankar, K. / Philmus, B. / Kinsland, C. / Sanders, J. / Begley, T.P. / Ealick, S.E.

Citation

Journal: J.Am.Chem.Soc. / Year: 2012
Title: Thiamin pyrimidine biosynthesis in Candida albicans : a remarkable reaction between histidine and pyridoxal phosphate.
Authors: Lai, R.Y. / Huang, S. / Fenwick, M.K. / Hazra, A. / Zhang, Y. / Rajashankar, K. / Philmus, B. / Kinsland, C. / Sanders, J.M. / Ealick, S.E. / Begley, T.P.

History

Deposition	Apr 23, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 3, 2017	Group: Non-polymer description
Revision 1.2	May 10, 2017	Group: Structure summary
Revision 1.3	Apr 3, 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 / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4esx.cif.gz	263.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4esx_validation.pdf.gz	437.2 KB	Display	wwPDB validaton report
Full document	4esx_full_validation.pdf.gz	437.7 KB	Display
Data in XML	4esx_validation.xml.gz	26.3 KB	Display
Data in CIF	4esx_validation.cif.gz	37.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/es/4esx ftp://data.pdbj.org/pub/pdb/validation_reports/es/4esx	HTTPS FTP

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Related structure data

Related structure data	4eswC C: citing same article (ref.)
Similar structure data	2vb8-2 1pxt-d 1afw-d 4h65-d 4gp4-d 4fa7-d 4g71-d 5w2p-1 4g72-d 1j3n-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

Deposited unit

A: Pyrimidine biosynthesis enzyme THI13

B: Pyrimidine biosynthesis enzyme THI13

77.9 kDa, 2 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)	55.157, 100.458, 126.198
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pyrimidine biosynthesis enzyme THI13 Mass: 38934.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Strain: WO-1 / Gene: CAWG_02199 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4YMW2
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.24 Å³/Da / Density % sol: 45.21 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 20% PEG 3350, 0.2 M ammonium chloride, pH 5.3, vapor diffusion, hanging drop, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.9795 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2012

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. all: 36139 / Num. obs: 36139 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / R_merge(I) obs: 0.105 / Χ²: 0.92 / Net I/σ(I): 5.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.2-2.24	5	0.69	1781	0.822	1	99.8
2.24-2.28	4.9	0.604	1775	0.85	1	99.4
2.28-2.32	4.5	0.586	1781	0.84	1	98.9
2.32-2.37	5.3	0.489	1795	0.833	1	99.9
2.37-2.42	5.3	0.446	1788	0.832	1	99.3
2.42-2.48	5.3	0.399	1802	0.86	1	99.9
2.48-2.54	5.2	0.347	1796	0.864	1	99.4
2.54-2.61	5.2	0.317	1802	0.855	1	99.8
2.61-2.69	5.1	0.28	1771	0.869	1	99.3
2.69-2.77	4.8	0.234	1812	0.886	1	99.3
2.77-2.87	4.7	0.194	1800	0.914	1	99
2.87-2.99	5.3	0.168	1789	0.912	1	99.4
2.99-3.12	5.3	0.136	1799	0.967	1	98.7
3.12-3.29	5.2	0.114	1806	0.972	1	99
3.29-3.49	5.1	0.086	1824	1.008	1	98.8
3.49-3.76	4.6	0.065	1797	1.064	1	98.8
3.76-4.14	5.4	0.056	1824	1.109	1	98.8
4.14-4.74	5.2	0.048	1830	1.123	1	97.7
4.74-5.97	4.8	0.046	1842	0.91	1	97.7
5.97-50	4.9	0.037	1925	0.881	1	96

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.11	data extraction
ADSC	Quantum	data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: The H66G mutant structure determined at 1.6 angstrom

Resolution: 2.2→48.349 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8304 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 23.54 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2275	1847	5.13 %	Random
R_work	0.1709	-	-	-
obs	0.1738	36004	98.94 %	-
all	-	36139	-	-

Solvent computation

Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.305 Å² / k_sol: 0.375 e/Å³

Displacement parameters

B_iso max: 92.68 Å² / B_iso mean: 34.4569 Å² / B_iso min: 14.91 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-7.4567 Å²	-0 Å²	0 Å²
2-	-	-2.4661 Å²	0 Å²
3-	-	-	9.9228 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→48.349 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4921	0	0	318	5239

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5046
X-RAY DIFFRACTION	f_angle_d	1.061	6839
X-RAY DIFFRACTION	f_chiral_restr	0.074	735
X-RAY DIFFRACTION	f_plane_restr	0.004	879
X-RAY DIFFRACTION	f_dihedral_angle_d	14.251	1863

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2-2.2595	0.2865	146	0.2034	2593	2739	100
2.2595-2.326	0.307	132	0.211	2578	2710	99
2.326-2.4011	0.2778	147	0.2025	2635	2782	100
2.4011-2.4869	0.2507	142	0.1896	2601	2743	100
2.4869-2.5865	0.2597	126	0.1931	2611	2737	100
2.5865-2.7042	0.2918	144	0.1923	2631	2775	100
2.7042-2.8467	0.2958	140	0.181	2603	2743	99
2.8467-3.0251	0.2151	150	0.1711	2610	2760	99
3.0251-3.2586	0.2472	146	0.173	2623	2769	99
3.2586-3.5864	0.2243	124	0.1656	2652	2776	99
3.5864-4.1052	0.2038	146	0.1501	2628	2774	99
4.1052-5.1711	0.1741	148	0.1309	2648	2796	98
5.1711-48.3604	0.2044	156	0.1874	2744	2900	97

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	0.0001	-0.0004	0.0052	-0.0001	0.0028	0.1019	-0.2369	0.3523	-0.4563	-1.0458	0.1252	0.2521	0.5664	-0.4429	0.0017	0.6116	0.0014	0.0297	0.5165	-0.1216	0.3743	44.3893	26.875	-0.5265
2	0.8414	-0.178	0.5946	0.8779	-0.3914	1.5477	0.0048	0.094	-0.2127	-0.084	-0.0072	-0.0487	0.0419	0.0492	0.0001	0.2037	0.0176	0.002	0.1876	-0.011	0.2284	34.5617	29.1651	20.038
3	2.1618	0.6494	-0.5218	1.7754	0.2263	2.391	0.1892	-0.3098	0.0243	0.2061	0.0182	0.105	-0.0341	-0.1326	0.0026	0.2036	0.0075	0.0187	0.2263	0.0151	0.1872	15.9258	38.1237	33.7972
4	0.929	0.299	0.0657	0.1311	0.154	0.5111	0.3787	-0.9246	0.1424	0.3915	-0.4329	-0.461	-0.2098	0.1039	0.0268	0.4198	-0.107	0.0175	0.461	-0.1293	0.4037	20.9114	39.5003	41.6033
5	1.6585	0.6385	0.0584	2.0897	0.5607	1.3661	0.0678	-0.1903	-0.3331	0.1609	-0.0838	-0.0101	0.0265	0.1186	0.0003	0.2265	0.0154	-0.0305	0.2254	0.0242	0.2538	40.39	32.6723	27.5932
6	0.7718	-0.268	-0.1718	0.588	0.0172	0.8555	0.0635	-0.4609	-0.7878	0.1527	-0.0871	-0.1115	0.0808	-0.006	0.0014	0.3144	0.0106	-0.0423	0.2703	0.1103	0.4471	29.5537	16.8702	30.919
7	1.6149	-0.2473	0.0871	1.3197	0.0288	1.8985	-0.072	0.0982	-0.2106	-0.0622	0.1048	0.0394	0.0302	-0.0017	-0.0001	0.2067	0.002	0.0064	0.2107	-0.0332	0.198	30.7816	38.328	4.487
8	1.7428	-0.2611	-0.6234	1.6745	0.0795	1.0139	0.0788	0.2389	0.2293	-0.1179	-0.0573	-0.1251	-0.1401	0.097	0.0001	0.2702	-0.0197	0.0123	0.259	0.0122	0.2503	50.4523	55.7216	6.6204
9	0.8512	-0.2554	0.3205	0.9753	-0.2318	0.1409	0.2057	0.3892	-0.0184	-0.299	-0.077	0.0975	-0.0716	-0.2004	0.0007	0.4291	0.0121	0.0372	0.3034	-0.044	0.3884	44.8456	64.2381	6.7452
10	0.9034	-0.7857	-0.0279	0.7952	-0.0587	1.7552	-0.1515	0.3033	-0.1462	-0.3671	0.3508	-0.0784	-0.0628	0.1026	0.0013	0.2326	-0.0473	0.0167	0.3561	-0.1109	0.2365	28.4984	39.1621	-3.6265
11	0.5566	0.2092	-0.4244	0.3997	-0.026	0.3781	0.0312	0.0187	0.4576	0.0216	-0.0602	0.2136	-0.2135	-0.1603	-0.0008	0.2925	0.0462	0.02	0.2413	0.0013	0.2671	23.3845	54.5717	10.5236
12	0.81	0.0004	-0.6534	0.6661	-0.3663	0.8849	-0.0041	0.6604	0.3006	-0.2703	0.1219	-0.158	-0.0346	-0.0628	0	0.3271	0.0016	-0.0134	0.4378	-0.0363	0.236	35.33	45.8168	-10.5714

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid -2:5)	A	-2 - 5
2	X-RAY DIFFRACTION	2	(chain A and resid 6:84)	A	6 - 84
3	X-RAY DIFFRACTION	3	(chain A and resid 85:173)	A	85 - 173
4	X-RAY DIFFRACTION	4	(chain A and resid 174:194)	A	174 - 194
5	X-RAY DIFFRACTION	5	(chain A and resid 195:266)	A	195 - 266
6	X-RAY DIFFRACTION	6	(chain A and resid 267:307)	A	267 - 307
7	X-RAY DIFFRACTION	7	(chain B and resid -1:84)	B	-1 - 84
8	X-RAY DIFFRACTION	8	(chain B and resid 85:171)	B	85 - 171
9	X-RAY DIFFRACTION	9	(chain B and resid 172:193)	B	172 - 193
10	X-RAY DIFFRACTION	10	(chain B and resid 194:224)	B	194 - 224
11	X-RAY DIFFRACTION	11	(chain B and resid 225:263)	B	225 - 263
12	X-RAY DIFFRACTION	12	(chain B and resid 264:307)	B	264 - 307

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