PDB-6tak: Crystal structure of Escherichia coli Orotate Phosphoribosyltrans...

ID or keywords:

Entry

Database: PDB / ID: 6tak

Title

Crystal structure of Escherichia coli Orotate Phosphoribosyltransferase in complex with Orotic acid and Sulfate at 1.25 Angstrom resolution

Components

Orotate phosphoribosyltransferase

Keywords

TRANSFERASE / Orotate phosphoribosyltransferase (OPRT) / Orotic acid / Sulfate

Function / homology

Function and homology information

pyrimidine ribonucleoside biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleotide biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.25 Å

Authors

Navas-Yuste, S. / Lopez-Estepa, M. / Gomez, S. / Fernandez, F.J. / Vega, M.C.

Funding support

Spain, 3items

Organization	Grant number	Country
Spanish Ministry of Economy and Competitiveness	CTQ2015-66206-C2-2-R	Spain
Spanish Ministry of Science, Innovation, and Universities	RTI2018-1018-102242-B-I00	Spain
Spanish National Research Council	2016E064	Spain

Citation

Journal: Acs Catalysis / Year: 2020
Title: Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by Means of X-ray Crystallography and Computational Simulations
Authors: Roca, M. / Navas-Yuste, S. / Zinovjev, K. / Lopez-Estepa, M. / Gomez, S. / Fernandez, F.J. / Vega, M.C. / Tunon, I.

History

Deposition	Oct 29, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 9, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6tak.cif.gz	333.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6tak.ent.gz		Display	PDB format
PDBx/mmJSON format	6tak.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6tak_validation.pdf.gz	4.1 MB	Display	wwPDB validaton report
Full document	6tak_full_validation.pdf.gz	4.1 MB	Display
Data in XML	6tak_validation.xml.gz	22.9 KB	Display
Data in CIF	6tak_validation.cif.gz	33.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ta/6tak ftp://data.pdbj.org/pub/pdb/validation_reports/ta/6tak	HTTPS FTP

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Related structure data

Related structure data	6taiSC 6tajC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3fz5-1 3fz5-2 3wpq-d 1oro-d 6tai-d 6dgn-d 4fq7-d 5d08-1 4jjp-d 6taj-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (4)

Deposited unit

AAA: Orotate phosphoribosyltransferase

BBB: Orotate phosphoribosyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	53.658, 69.469, 104.383
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab

#1: Protein	Orotate phosphoribosyltransferase / OPRTase Mass: 23594.967 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: pyrE, b3642, JW3617 / Plasmid: pET21b / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P0A7E3, orotate phosphoribosyltransferase
#2: Chemical	ChemComp-ORO / OROTIC ACID Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₄N₂O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.44 % / Description: Cubic, bipyramidal, and rhombohedral plates
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 2.1 M (NH4)2SO4, 0.2 M NaCl, 0.3 M sodium citrate (pH 4.8)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2019 / Details: Kirkpatrick-Baez (KB) focusing mirrors
Radiation	Monochromator: Channel-cut Si(111), cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 1.25→47.72 Å / Num. obs: 452457 / % possible obs: 95.9 % / Redundancy: 4.3 % / B_iso Wilson estimate: 17.56 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.048 / R_pim(I) all: 0.025 / R_rim(I) all: 0.054 / Net I/σ(I): 13.2
Reflection shell	Resolution: 1.25→1.28 Å / Redundancy: 2.3 % / R_merge(I) obs: 1.386 / Num. unique obs: 12799 / CC_1/2: 0.292 / R_pim(I) all: 1.001 / R_rim(I) all: 1.722 / % possible all: 68.8

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Processing

Software

Name	Version	Classification
PHENIX	1.17_3644	refinement
XDS	Mar 15, 2019 BUILT=20190315	data reduction
Aimless	0.7.4	data scaling
PHASER	2.8.2 (svn 8393)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: wwPDB 6TAI

6tai

Resolution: 1.25→47.72 Å / SU ML: 0.2551 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.2545

	R_factor	Num. reflection	% reflection
R_free	0.2059	1982	1.96 %
R_work	0.1811	-	-
obs	0.1816	101164	92.84 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 26.23 Å²

Refinement step

Cycle: LAST / Resolution: 1.25→47.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3264	0	103	375	3742

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0118	3550
X-RAY DIFFRACTION	f_angle_d	1.2132	4813
X-RAY DIFFRACTION	f_chiral_restr	0.0818	529
X-RAY DIFFRACTION	f_plane_restr	0.008	618
X-RAY DIFFRACTION	f_dihedral_angle_d	15.8871	1339

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 (%)
1.25-1.28	0.5036	91	0.4621	4568	X-RAY DIFFRACTION	60.44
1.28-1.31	0.591	86	0.5346	4155	X-RAY DIFFRACTION	55.31
1.31-1.35	0.4634	143	0.417	7151	X-RAY DIFFRACTION	94.81
1.35-1.4	0.3988	149	0.3839	7471	X-RAY DIFFRACTION	98.94
1.4-1.45	0.2963	151	0.3054	7567	X-RAY DIFFRACTION	99.6
1.45-1.5	0.2916	149	0.2423	7504	X-RAY DIFFRACTION	99.62
1.5-1.57	0.2753	151	0.2237	7557	X-RAY DIFFRACTION	99.45
1.57-1.66	0.239	152	0.2023	7605	X-RAY DIFFRACTION	99.92
1.66-1.76	0.2234	151	0.1695	7563	X-RAY DIFFRACTION	99.87
1.76-1.89	0.2104	152	0.1756	7597	X-RAY DIFFRACTION	99.61
1.89-2.09	0.2197	146	0.1814	7358	X-RAY DIFFRACTION	96.06
2.09-2.39	0.2103	148	0.158	7438	X-RAY DIFFRACTION	97
2.39-3.01	0.1716	154	0.1547	7731	X-RAY DIFFRACTION	99.58
3.01-47.72	0.1526	159	0.1496	7917	X-RAY DIFFRACTION	98.63

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	1.05069470278	-0.779942305585	-0.262563862863	1.74410586755	-0.336983313367	1.23578484555	-0.0208647867836	-0.450199384316	-0.174365060285	0.373853807357	0.0347929521996	0.0222515502095	0.125965869248	-0.195573748361	-0.0339835248552	0.289113534833	-0.0473205411712	-0.0191431235095	0.276735946364	0.044793396077	0.0772896863159	8.05182208587	5.6018785373	36.6765979497
2	1.04004598474	-0.203717508756	0.559316927248	0.763746119377	0.340455841895	1.60571771143	0.0185517509607	-0.0801376669944	-0.0351593226242	-0.0272746862831	-0.0444639333697	-0.00359401639847	-0.0738217567708	-0.0279145221883	0.0133572706939	0.177947114098	-0.00430840850507	-0.00351233249919	0.124872411091	0.0158743225113	0.0310236480835	7.28867883378	6.33464256975	19.5434534665
3	5.95982093584	1.32721548076	-2.01038834665	3.0836223202	-1.30799428041	4.10231674537	-0.310433967152	0.373961607159	-0.795106380556	-0.441475712254	0.154491137716	0.308945677181	0.658347359179	-0.0466644183146	0.237066246051	0.378625543848	0.0362636304101	-0.0445659938964	0.224580237643	-0.0833225309734	0.231291756182	7.2460364651	-7.91571535835	9.82948571191
4	1.19401571745	-0.898137261622	-1.27561733256	1.89075206769	-0.647653710103	9.13634724647	0.0414743975171	-0.0244416137698	-0.308075234773	0.391519385817	-0.186416585613	0.0497953232193	-0.0454407571703	0.0916034265318	0.000746613303271	0.250743463985	-0.0150089795246	-0.00438602306009	0.18131708405	-0.00548886888994	0.142411477097	13.8452021298	-1.56456419448	21.682682305
5	2.75838621949	-0.958665999083	-1.97209896789	1.9998787364	0.92919394629	1.4464852146	-0.167548023854	-0.280832445254	-0.58977533012	0.205475503246	-0.500852246366	0.0649187437617	0.934828210734	0.849590766708	0.280298817842	0.460860077039	0.00383192214444	-0.027516197761	0.377902662066	0.0512394409335	0.208624464359	15.6709995031	-10.1523109472	16.1796948731
6	0.846758253743	0.505615316371	0.48308593879	0.328293477446	0.487449910087	2.34753672591	0.00671409284991	-0.0376280677426	-0.236833317255	0.108051210651	0.0639658106529	-0.159148302061	0.296922527277	0.687478304817	-0.0535560164792	0.293338059776	0.0663390807455	-0.016340043497	0.283155097912	0.0115365014158	0.094289876451	20.6749808697	-2.02685276835	27.5075633788
7	0.757327636842	0.138351605799	0.0208106151898	1.49573009193	-0.519299445113	2.08546226574	-0.0785299037784	-0.448771271453	0.0110789151817	0.625625386564	0.230981885219	0.0407262551437	-0.166892452741	-0.147648665819	0.0454925379565	0.423188547685	0.0607031413851	-0.0178441882537	0.336793565394	0.0080416283203	0.0878809272616	14.5522338411	7.0761772069	44.5698078449
8	2.96841388374	0.758012720101	0.365293444063	1.86513056328	-0.0536284437375	2.47089870333	0.0100345942815	0.248801642371	-0.175039522388	-0.173518642677	0.0447913467342	-0.0149424138866	-0.00336113812974	-0.0220975676489	-0.05455159441	0.231183702571	0.0274496420587	-0.0269048706089	0.15759010619	0.0125754045496	0.0539786668547	-7.62467957641	4.44890195987	-4.26043943016
9	1.5507585039	0.0101954034071	0.338059802447	0.436577465116	0.0552156224186	3.03092828832	0.0199077687967	0.0173105595897	-0.00425587858829	-0.0312157827108	0.0175721232918	0.0194974233568	-0.076344963908	0.000469725356292	-0.0268358099496	0.179981162022	0.00896354527615	-0.015878487978	0.0976438137964	0.0151827959495	0.0529808000322	-5.88945575837	7.7408669409	6.15165916474
10	1.24690628142	-0.0906571787761	-0.10350269966	2.35760408945	-0.0733453150306	2.23499612948	0.00862486994432	-0.177200859985	-0.157429145158	0.0492110359775	-0.0137777693715	-0.0420880126699	0.0935806072717	-0.157624734868	-0.0303052622158	0.197635633792	0.0032633284982	-0.0054246777531	0.163885442474	0.0159373175186	0.0660159351641	-8.6714022364	0.467744280042	19.5056682365
11	4.83528072408	0.196197804052	-1.43427651356	4.41998888345	-2.57204767058	1.85862312929	0.0233227727295	0.464735179827	-0.174503014163	-0.722239553965	0.124011191626	0.231094090392	0.0195747668718	-0.193929618624	-0.0885195061976	0.345832824599	0.00860523774654	-0.0432682200492	0.218102711636	0.0388390011524	0.159420307418	-15.7439129301	-9.65775267616	16.9743457809
12	0.917917412994	0.0667695916564	-0.794940756219	0.0622413446516	-0.321522096361	4.03532286927	-0.087148584917	0.0660787543009	-0.184429765689	-0.131185916966	0.0429262982144	0.0821892852003	0.337614909961	-0.354771789803	0.0585962642531	0.265350526254	-0.0338994494824	-0.0145347533275	0.180368619567	0.0197878906641	0.114500505818	-19.1397379391	-3.16226377669	5.50354448556
13	3.42624394844	1.9333254164	-2.34801471583	2.17582364143	-2.31795890653	3.55367632422	-0.0556214965475	0.00200790932451	-0.0139457949743	-0.115623665647	0.0457053596899	0.152313176938	0.0870083995505	-0.336283889613	0.00410558573119	0.248075321514	0.0215329292971	-0.0305514484341	0.260441768834	0.0172679923483	0.0689422542787	-21.7370058386	-1.36205163926	7.3254659227
14	2.93243793162	0.356081038252	0.765634912909	5.30877842261	0.813451267138	3.53710531291	0.0956136215109	0.364856219842	0.151001340479	-0.138965772559	0.00501531182954	-0.197954452946	-0.073035776756	-0.123544535141	-0.06659220174	0.256981313862	0.0386820282205	-0.0258037459137	0.187210158144	0.0312684335466	0.0489291272802	-14.6122541839	6.03271461777	-11.7477100513

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'AAA' and (resid 1 through 32 )
2	X-RAY DIFFRACTION	2	chain 'AAA' and (resid 33 through 98 )
3	X-RAY DIFFRACTION	3	chain 'AAA' and (resid 99 through 118 )
4	X-RAY DIFFRACTION	4	chain 'AAA' and (resid 119 through 130 )
5	X-RAY DIFFRACTION	5	chain 'AAA' and (resid 131 through 143 )
6	X-RAY DIFFRACTION	6	chain 'AAA' and (resid 144 through 183 )
7	X-RAY DIFFRACTION	7	chain 'AAA' and (resid 184 through 213 )
8	X-RAY DIFFRACTION	8	chain 'BBB' and (resid 1 through 32 )
9	X-RAY DIFFRACTION	9	chain 'BBB' and (resid 33 through 60 )
10	X-RAY DIFFRACTION	10	chain 'BBB' and (resid 61 through 130 )
11	X-RAY DIFFRACTION	11	chain 'BBB' and (resid 131 through 142 )
12	X-RAY DIFFRACTION	12	chain 'BBB' and (resid 143 through 165 )
13	X-RAY DIFFRACTION	13	chain 'BBB' and (resid 166 through 183 )
14	X-RAY DIFFRACTION	14	chain 'BBB' and (resid 184 through 213 )

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