PDB-7r8y: Ancestral protein AncThEn of Phosphomethylpyrimidine kinases family

ID or keywords:

Entry

Database: PDB / ID: 7r8y

Title

Ancestral protein AncThEn of Phosphomethylpyrimidine kinases family

Components

Phosphomethylpyrimidine Kinase

Keywords

TRANSFERASE / ancestral protein reconstruction / 5-Phosphohydroxymethyl-2-methylpyrimidine kinase / Phosphomethylpyrimidine kinases family / enzyme evolution

Function / homology

4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Munoz, S. / Maturana, P. / Gonzalez-Ordenes, F. / Cea, P. / Castro-Fernandez, V.

Funding support

Chile, 3items

Organization	Grant number	Country
Comision Nacional Cientifica y Technologica (CONICYT)	1150460	Chile
Comision Nacional Cientifica y Technologica (CONICYT)	3160332	Chile
Comision Nacional Cientifica y Technologica (CONICYT)	EQM 120208	Chile

Citation

Journal: Mol.Biol.Evol. / Year: 2024
Title: Deciphering Structural Traits for Thermal and Kinetic Stability across Protein Family Evolution through Ancestral Sequence Reconstruction
Authors: Cea, P.A. / Perez, M. / Herrera, S.M. / Munoz, S.M. / Fuentes-Ugarte, N. / Coche-Miranda, J. / Maturana, P. / Guixe, V. / Castro-Fernandez, V.

History

Deposition	Jun 27, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 29, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Aug 21, 2024	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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7r8y.cif.gz	194.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7r8y.ent.gz	138.4 KB	Display	PDB format
PDBx/mmJSON format	7r8y.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/r8/7r8y ftp://data.pdbj.org/pub/pdb/validation_reports/r8/7r8y	HTTPS FTP

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Related structure data

Related structure data	7r8zC 1jxhS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphomethylpyrimidine Kinase

B: Phosphomethylpyrimidine Kinase

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	113.316, 113.316, 112.233
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2
Space group name Hall	P4n2n
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/2 #3: y+1/2,-x+1/2,z+1/2 #4: x+1/2,-y+1/2,-z+1/2 #5: -x+1/2,y+1/2,-z+1/2 #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z

#1: Protein	Phosphomethylpyrimidine Kinase Mass: 30406.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: phosphooxymethylpyrimidine kinase
#2: Chemical	ChemComp-HMH / 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE Mass: 139.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₉N₃O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.48 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop Details: Protein condition: Protein 20 mg/mL, HMP 1 mM, ADP 1 mM, HEPES 50 mM pH 8.0, NaCl 150 mM and 2-mercaptoethanol 5 mM Reservoir condition: 2-Propanol 14% v/v, Calcium chloride dihydrate 0.14 ...Details: Protein condition: Protein 20 mg/mL, HMP 1 mM, ADP 1 mM, HEPES 50 mM pH 8.0, NaCl 150 mM and 2-mercaptoethanol 5 mM Reservoir condition: 2-Propanol 14% v/v, Calcium chloride dihydrate 0.14 M, Sodium acetate 0.07 M, Glycerol 30% v/v.

Crystal

Density Matthews: 2.96 Å³/Da / Density % sol: 58.48 %

Crystal grow

Temperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein condition: Protein 20 mg/mL, HMP 1 mM, ADP 1 mM, HEPES 50 mM pH 8.0, NaCl 150 mM and 2-mercaptoethanol 5 mM Reservoir condition: 2-Propanol 14% v/v, Calcium chloride dihydrate 0.14 ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45867 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 5, 2019
Radiation	Monochromator: Double Crystal Monochromator - Water-cooled Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.45867 Å / Relative weight: 1
Reflection	Resolution: 3.2→45.96 Å / Num. obs: 12568 / % possible obs: 99.83 % / Redundancy: 25.8 % / B_iso Wilson estimate: 82.69 Å² / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.41 / R_pim(I) all: 0.08148 / R_rim(I) all: 0.4181 / Net I/σ(I): 10.88
Reflection shell	Resolution: 3.2→3.314 Å / Redundancy: 27.3 % / R_merge(I) obs: 3.331 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 1223 / CC_1/2: 0.544 / CC star: 0.84 / R_pim(I) all: 0.6455 / R_rim(I) all: 3.394 / % possible all: 99.92

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
MxCuBE		data collection
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1JXH

1jxh

Resolution: 3.2→45.96 Å / SU ML: 0.4556 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7106 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2539	606	4.83 %
R_work	0.2322	11949	-
obs	0.2332	12555	99.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 81.42 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→45.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3099	0	10	0	3109

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0056	3146
X-RAY DIFFRACTION	f_angle_d	0.9754	4281
X-RAY DIFFRACTION	f_chiral_restr	0.0643	534
X-RAY DIFFRACTION	f_plane_restr	0.0061	556
X-RAY DIFFRACTION	f_dihedral_angle_d	15.2155	1112

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 (%)
3.2-3.52	0.3465	167	0.3173	2886	X-RAY DIFFRACTION	99.97
3.52-4.03	0.2638	115	0.2455	2972	X-RAY DIFFRACTION	99.9
4.03-5.08	0.2252	171	0.2011	2954	X-RAY DIFFRACTION	100
5.08-45.96	0.2389	153	0.2228	3137	X-RAY DIFFRACTION	99.73

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	0.248020305876	-0.324293600986	0.0359508308422	1.01312359164	0.582157866689	0.429775357631	-0.134685970439	0.0275831379881	-0.448198680147	-0.348160836596	-0.169887723412	-0.0346952785928	-0.000961588137402	0.0415152429554	-0.0588373996974	0.759940746184	0.0833362253456	0.251151245894	0.414816932859	0.115357869279	0.647379986095	19.6851727642	-14.6937286678	36.9871951295
2	0.0912341966251	-0.119617407051	0.0896869041383	0.360683237379	-0.0725844665599	0.414189511853	-0.148034444808	0.0506957417713	-0.331963388523	-0.202361971715	-0.110422931286	-0.100914051987	-0.448807772854	-0.205200614343	-1.97667553167E-7	0.783272254529	0.0563813895217	0.17666870608	0.417180445889	-0.0252902401343	0.478162235933	13.0449599906	-8.78693730136	29.6103217893
3	0.829259192975	0.565801025669	-0.0542314248684	0.357282578455	-0.254249242266	0.935138223699	-0.100029446282	-0.277302283829	0.139943714984	-1.24026964412	-0.373135076955	0.578053564394	-1.25399159279	-0.33124242583	-0.731782831431	1.10422371014	0.147636084229	0.243793152648	0.225897815145	0.237080147188	0.296308695651	12.9306286218	-1.05983350381	29.6025864113
4	0.662535406519	-0.0725510480823	-0.0399309040865	0.136290565751	0.308681634621	0.716570677657	-0.291037998594	-0.150003699601	-0.126148360347	-0.367022179954	0.345769103023	-0.185404970963	-0.442036079365	0.0379115674462	0.236901148815	0.747002418864	0.0129369601051	0.246303666748	0.340740568727	0.168538774985	0.683611489072	23.5655697022	1.17476672027	37.2463985731
5	0.150883355583	0.191271642484	0.333148524868	0.276580020581	0.178331406479	0.424697481108	-0.173380447581	-0.495614299373	0.0497251701094	-0.438760257099	0.0744285301978	0.161541380932	-0.688248898355	0.0943126822683	-0.000126874636812	0.707890007746	0.0893183819553	0.149382390407	0.537850885756	0.0341066306673	0.696842509588	22.0408051111	8.43638301994	48.7830236272
6	0.666038616607	0.591413836637	0.131676748839	0.914109704288	-0.651470205672	0.557732156751	0.0360539265618	-0.401387330207	-0.125618227462	-0.254125411707	-0.208839283119	-0.0337614137846	-0.392896249061	-0.026436557073	0.00170525514929	0.523870541832	0.161126880482	0.0836722106726	0.385077079223	0.0849086788824	0.245448313663	12.4848558433	-5.29629412533	51.7356961381
7	0.702488580024	0.661662902195	-0.131496776683	0.559166512486	-0.176872375143	0.0999427090728	-0.661079386748	0.194433341976	-0.382163279054	-0.220032961757	0.477490803021	0.285731107946	0.539274628513	-0.23043599432	-0.084346144503	1.10610011239	0.0938985149956	0.448729063466	0.460566675409	-0.0640914850023	0.818444181625	18.3078150555	-25.6048226946	34.1733043808
8	0.553819068235	0.165109776041	0.422547255118	0.159547919073	0.0707713550556	0.55938591917	-0.698459400883	-0.633095036774	-0.364672139426	-0.0625286168853	0.000588467477962	0.442916329248	-0.290321637363	-0.0352486986214	-0.191442463999	1.10470102592	0.259810387949	0.421292467898	0.653073786576	0.119963625873	0.757880683043	16.9629404474	-25.9810536589	37.9925473945
9	1.32747954449	-0.170459134816	1.19151651242	0.376468561746	-0.237835051812	1.10345998773	-0.259195158397	0.874219169111	-0.333094577469	-0.33823861069	-0.128522194053	-0.136933203005	-0.354406290585	0.688948946598	-0.0291463704046	1.20605446739	0.164809310114	0.425941481581	0.425667202277	0.101773239983	1.14052224351	26.0213725862	-20.028894006	26.08567432
10	0.28743284734	0.261462593142	0.287562745888	0.326158225362	0.0707791493585	0.390456226514	-0.213032159784	0.475670788441	-0.153186898894	0.00160589710266	0.81929249896	-0.130201411656	-0.167056127049	0.496871670688	0.432224314373	1.23154025959	0.571745294381	0.825502238581	-0.179495766279	-0.61201928943	0.510989964041	25.6538968489	-29.6720009019	33.1298496285
11	0.070958895296	-0.0694451304434	0.0112566667006	0.0176218185997	0.0470044913577	0.052260580209	-0.182108497847	-0.0593446108032	0.318038946696	-0.314464635383	0.601396168669	-0.887574240487	0.367512221329	0.69375625421	-3.21716404566E-6	1.37764698965	0.219061206569	0.259549141697	0.626160257845	-0.0423368670719	0.915126801296	34.0839660223	-30.5560906598	27.074716314
12	2.50630046705	0.774243859373	0.0458948419267	0.534108130108	0.0162647456292	0.165710838171	-0.775469993662	0.398483965884	0.0923475304988	0.401306040399	0.470237425744	-0.152694749489	0.522589404808	-0.197252662737	-0.183899259479	1.17741419217	0.186076689856	0.486204607713	0.466437854498	-0.0432254760033	0.830117486602	25.0073631607	-36.2844027082	24.0905239284
13	0.864210599215	-0.817237867169	0.345282372801	0.791085914898	-0.292454890602	0.179722880903	0.734384542951	0.357509120147	-1.1454234811	0.608626993306	-0.0848006531287	0.532708101854	0.189538542919	-0.411478175522	0.699885988487	1.02112103735	0.296020800446	0.158111669343	0.495351110285	-0.227158632654	1.08595776243	16.558642239	-45.7619741346	16.4146436354
14	-0.00946771089882	0.0491673735092	-0.0312380355669	0.0465863702691	-0.062406176606	0.279240205709	0.538845833352	0.676296378246	-0.0175436344305	0.520986902512	-0.671372814652	0.748462639757	-0.361700894533	0.604355732774	-0.00646328653963	0.908987050195	-0.00958121780493	0.182154057637	0.460078138502	-0.021850994698	1.10897903756	12.4903587391	-44.3553191567	23.9458043607
15	0.0602886016561	0.0310648241308	0.0157623333063	0.056307566165	0.116438976694	0.0552292202034	-0.0864343018851	-0.157569036778	-0.372621694473	-0.0561550988566	0.177568066894	0.312084642793	0.172907183287	-0.0665618988134	1.35258771823E-6	1.39151068798	0.0476924474202	0.385814468231	0.589240148574	0.0139745269309	0.972477240749	15.3223978745	-42.3264836404	34.5943562967
16	0.438091494781	0.0908794110161	0.809354448647	0.0319667401365	0.143264955237	1.53458578168	-0.322326438538	-0.676026544518	-0.593446268336	0.410761065341	-0.638583931237	-0.466267110945	0.719786907441	-1.02553462435	-0.0587140491854	1.66720108886	-0.130105517753	0.620681937273	0.807013807964	-0.0411359727879	1.97876537897	8.45061081867	-40.6998084848	36.6061621671

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 81 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82 through 102 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 103 through 137 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 138 through 188 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 189 through 243 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 17 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 18 through 36 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 37 through 65 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 66 through 81 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 82 through 94 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 95 through 137 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 138 through 165 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 166 through 184 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 185 through 225 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 226 through 240 )

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