PDB-4esw: Crystal structure of C. albicans Thi5 H66G mutant

ID or keywords:

Entry

Database: PDB / ID: 4esw

Title

Crystal structure of C. albicans Thi5 H66G mutant

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 /

SAD / Resolution: 1.6 Å

Authors

Fenwick, M.K. / Huang, S. / 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	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2	Feb 28, 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

-
Download

PDBx/mmCIF format	4esw.cif.gz	300.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4esw.ent.gz	244.3 KB	Display	PDB format
PDBx/mmJSON format	4esw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4esw_validation.pdf.gz	451.6 KB	Display	wwPDB validaton report
Full document	4esw_full_validation.pdf.gz	453.1 KB	Display
Data in XML	4esw_validation.xml.gz	33.2 KB	Display
Data in CIF	4esw_validation.cif.gz	52.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/es/4esw ftp://data.pdbj.org/pub/pdb/validation_reports/es/4esw	HTTPS FTP

-
Related structure data

Related structure data	4esxC C: citing same article (ref.)
Similar structure data	4h67-4 4h6d-1 5k7x-1 4h67-1 4ubu-4 4h6d-4 5k7x-3 6hfe-1 4h6d-3 4ubt-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pyrimidine biosynthesis enzyme THI13

B: Pyrimidine biosynthesis enzyme THI13

hetero molecules

77.6 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)	55.386, 99.474, 126.389
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: 38625.164 Da / Num. of mol.: 2 / Mutation: H66G 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: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 818 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.42 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 15% PEG 4K, 100 mM citrate, pH 5.3, vapor diffusion, hanging drop, temperature 295K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	24-ID-C	1	0.9792
SYNCHROTRON	APS	24-ID-C	2	0.9194

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315	1	CCD	Feb 11, 2012
ADSC QUANTUM 315	2	CCD	Feb 11, 2012

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Si(111)	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9792	1
2	0.9194	1

Reflection

Redundancy: 7.8 % / Av σ(I) over netI: 22.71 / Number: 831131 / R_merge(I) obs: 0.119 / Χ²: 1.02 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 106130 / % possible obs: 99.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.09	50	99.8	1	0.037	0.876	8
3.25	4.09	99.9	1	0.053	1.01	8
2.84	3.25	100	1	0.084	1.121	8.2
2.58	2.84	99.8	1	0.132	1.114	7.7
2.39	2.58	99.9	1	0.186	1.071	8
2.25	2.39	100	1	0.252	1.059	8.1
2.14	2.25	99.8	1	0.324	1.052	7.4
2.05	2.14	99.9	1	0.444	1.025	7.8
1.97	2.05	99.9	1	0.663	0.967	7.8
1.9	1.97	98.9	1	0.98	0.945	7.3

Reflection

Resolution: 1.6→50 Å / Num. all: 92106 / Num. obs: 92106 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / R_merge(I) obs: 0.06 / Χ²: 0.912 / Net I/σ(I): 8.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.6-1.63	4.3	0.481	4560	0.897	1,2	99.2
1.63-1.66	4.3	0.427	4545	0.89	1,2	99.5
1.66-1.69	4.2	0.375	4581	0.913	1,2	99.8
1.69-1.72	4.2	0.315	4571	0.889	1,2	99.8
1.72-1.76	4.2	0.273	4553	0.882	1,2	99.7
1.76-1.8	4.2	0.248	4594	0.903	1,2	99.8
1.8-1.85	4	0.214	4593	0.897	1,2	99
1.85-1.9	3.9	0.172	4443	0.952	1,2	97
1.9-1.95	4.5	0.163	4597	0.986	1,2	99.8
1.95-2.02	4.5	0.13	4597	0.92	1,2	99.8
2.02-2.09	4.5	0.106	4600	0.937	1,2	99.9
2.09-2.17	4.4	0.087	4620	0.916	1,2	99.9
2.17-2.27	4.3	0.077	4635	0.968	1,2	99.5
2.27-2.39	4	0.059	4466	0.877	1,2	96.9
2.39-2.54	4.5	0.052	4633	0.881	1,2	99.2
2.54-2.74	4.6	0.046	4628	0.903	1,2	99.6
2.74-3.01	4.5	0.039	4676	0.915	1,2	99.7
3.01-3.45	4.1	0.033	4609	0.993	1,2	97.5
3.45-4.34	4.5	0.026	4713	0.937	1,2	99.1
4.34-50	4.2	0.023	4892	0.786	1,2	98.2

-
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
MLPHARE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.6→39.084 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8995 / SU ML: 0.18 / σ(F): 1.35 / Phase error: 16.83 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1906	4617	5.02 %	Random
R_work	0.1622	-	-	-
obs	0.1637	92025	99.04 %	-
all	-	92106	-	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.568 Å² / k_sol: 0.391 e/Å³

Displacement parameters

B_iso max: 75.6 Å² / B_iso mean: 16.6677 Å² / B_iso min: 4.07 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.5524 Å²	0 Å²	-0 Å²
2-	-	0.5571 Å²	-0 Å²
3-	-	-	-0.0047 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→39.084 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5391	0	26	818	6235

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5835
X-RAY DIFFRACTION	f_angle_d	1.055	7938
X-RAY DIFFRACTION	f_chiral_restr	0.074	846
X-RAY DIFFRACTION	f_plane_restr	0.005	1052
X-RAY DIFFRACTION	f_dihedral_angle_d	13.476	2209

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.6176	0.2091	146	0.1987	2790	2936	96
1.6176-1.6366	0.2503	168	0.1965	2856	3024	99
1.6366-1.6566	0.249	158	0.2036	2890	3048	99
1.6566-1.6775	0.2194	166	0.1888	2910	3076	100
1.6775-1.6996	0.2193	149	0.1859	2906	3055	100
1.6996-1.7229	0.2225	172	0.1759	2844	3016	100
1.7229-1.7475	0.2293	156	0.1718	2930	3086	100
1.7475-1.7736	0.1985	144	0.1682	2911	3055	100
1.7736-1.8013	0.2023	141	0.1667	2888	3029	100
1.8013-1.8308	0.2075	172	0.1684	2880	3052	99
1.8308-1.8624	0.2031	144	0.1605	2877	3021	97
1.8624-1.8963	0.1788	143	0.1513	2833	2976	98
1.8963-1.9327	0.2154	134	0.1571	2932	3066	100
1.9327-1.9722	0.1952	140	0.1567	2927	3067	100
1.9722-2.0151	0.1879	144	0.163	2915	3059	100
2.0151-2.0619	0.213	142	0.1601	2926	3068	100
2.0619-2.1135	0.1607	156	0.1556	2920	3076	100
2.1135-2.1706	0.1961	148	0.1531	2930	3078	100
2.1706-2.2345	0.1793	148	0.1542	2936	3084	100
2.2345-2.3066	0.1824	137	0.1536	2956	3093	99
2.3066-2.3891	0.2002	167	0.1532	2771	2938	96
2.3891-2.4847	0.1929	153	0.1509	2922	3075	99
2.4847-2.5978	0.1914	155	0.1626	2937	3092	100
2.5978-2.7347	0.2067	159	0.172	2937	3096	100
2.7347-2.906	0.1839	164	0.1711	2951	3115	100
2.906-3.1303	0.1803	164	0.1724	2956	3120	100
3.1303-3.4451	0.2041	144	0.1636	2905	3049	97
3.4451-3.9432	0.1622	160	0.1456	2966	3126	99
3.9432-4.9664	0.1442	170	0.1339	3011	3181	100
4.9664-39.0955	0.2119	173	0.1895	3095	3268	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	0.8879	-0.0903	-0.1363	0.4174	-0.1375	0.522	0.0344	-0.0129	-0.0143	0.0313	0.0002	0.0236	-0.0184	-0.0358	-0.0249	0.0551	-0.0043	-0.0054	0.0389	-0.0042	0.0486	25.7548	33.36	27.8069
2	1.0206	0.1629	-0.1284	0.8159	-0.042	0.5191	0.0097	-0.0455	-0.1119	0.0238	-0.0135	-0.0758	0.0222	0.0356	0.0011	0.0475	0.0076	-0.0112	0.044	0.004	0.0536	37.6427	26.8099	29.1314
3	1.4979	0.5981	-0.6386	1.6902	-0.555	2.0706	0.022	-0.328	-0.0949	0.369	-0.006	-0.0116	0.1965	-0.0658	-0.0207	0.2442	0.0106	-0.0104	0.2489	0.006	0.0451	35.2753	31.5835	46.3761
4	0.8081	-0.1956	0.0673	1.1526	-0.0562	1.1377	-0.0124	0.0917	-0.0906	-0.0502	0.0391	-0.0084	0.0318	0.0288	-0.01	0.0394	-0.0009	0.0035	0.045	-0.0102	0.0364	30.7784	38.0712	4.4673
5	1.3056	-0.2464	-0.2902	1.1047	0.1187	0.7457	0.0566	0.1223	0.078	-0.0622	-0.0439	-0.0266	-0.1214	0.028	0.0081	0.0606	-0.0235	0.0096	0.0414	0.0026	0.06	48.8573	57.0203	6.3797
6	0.8076	0.0775	-0.3248	0.6159	-0.0137	0.6775	0.0109	0.1791	0.0152	-0.0833	0.0291	0.0273	-0.0568	-0.0863	-0.0325	0.0479	0.0003	-0.0015	0.078	0.0008	0.0339	30.0002	46.9618	-1.9536
7	3.9397	0.6138	-0.6285	3.1245	-0.2152	3.5244	0.0041	0.4042	0.333	-0.3718	0.1148	-0.1325	-0.6771	0.0147	-0.1041	0.2736	-0.0118	0.0246	0.1482	0.0529	0.2072	31.5283	65.4668	-2.0667

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 -2:207)	A	-2 - 207
2	X-RAY DIFFRACTION	2	(chain A and resid 208:308)	A	208 - 308
3	X-RAY DIFFRACTION	3	(chain A and resid 309:339)	A	309 - 339
4	X-RAY DIFFRACTION	4	(chain B and resid -2:85)	B	-2 - 85
5	X-RAY DIFFRACTION	5	(chain B and resid 86:199)	B	86 - 199
6	X-RAY DIFFRACTION	6	(chain B and resid 200:309)	B	200 - 309
7	X-RAY DIFFRACTION	7	(chain B and resid 310:339)	B	310 - 339

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi