PDB-6r02: Psychrobacter arcticus ATP phosphoribosyltransferase bound to his...

ID or keywords:

Entry

Database: PDB / ID: 6r02

Title

Psychrobacter arcticus ATP phosphoribosyltransferase bound to histidine and PRPP

Components

ATP phosphoribosyltransferase
ATP phosphoribosyltransferase regulatory subunit

Keywords

TRANSFERASE / ATPPRT / histidine / phosphoribosyltransferase

Function / homology

Function and homology information

ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / L-histidine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function

Biological species

Psychrobacter arcticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.65 Å

Authors

Alphey, M.S. / da Silva, R.G. / Thomson, C.M.

Citation

Journal: Biochemistry / Year: 2019
Title: Mapping the Structural Path for Allosteric Inhibition of a Short-Form ATP Phosphoribosyltransferase by Histidine.
Authors: Thomson, C.M. / Alphey, M.S. / Fisher, G. / da Silva, R.G.

History

Deposition	Mar 12, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 7, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6r02.cif.gz	893.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6r02.ent.gz	746.7 KB	Display	PDB format
PDBx/mmJSON format	6r02.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6r02_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	6r02_full_validation.pdf.gz	1.5 MB	Display
Data in XML	6r02_validation.xml.gz	77.4 KB	Display
Data in CIF	6r02_validation.cif.gz	102.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r0/6r02 ftp://data.pdbj.org/pub/pdb/validation_reports/r0/6r02	HTTPS FTP

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Related structure data

Related structure data	6fttS S: Starting model for refinement
Similar structure data	6fua-1 6ftt-d 6fu2-1 5m8h-d 6jpl-d 6e2q-d 6jp6-d 3gut-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: ATP phosphoribosyltransferase regulatory subunit

B: ATP phosphoribosyltransferase regulatory subunit

C: ATP phosphoribosyltransferase regulatory subunit

D: ATP phosphoribosyltransferase regulatory subunit

E: ATP phosphoribosyltransferase

F: ATP phosphoribosyltransferase

G: ATP phosphoribosyltransferase

H: ATP phosphoribosyltransferase

hetero molecules

276 kDa, 8 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)	93.253, 147.310, 99.327
Angle α, β, γ (deg.)	90.000, 103.110, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	VAL	VAL	A	A	0 - 387	1 - 388
2	1	GLY	GLY	VAL	VAL	B	B	0 - 387	1 - 388
1	2	GLY	GLY	VAL	VAL	A	A	0 - 387	1 - 388
2	2	GLY	GLY	VAL	VAL	C	C	0 - 387	1 - 388
1	3	GLY	GLY	VAL	VAL	A	A	0 - 387	1 - 388
2	3	GLY	GLY	VAL	VAL	D	D	0 - 387	1 - 388
1	4	GLY	GLY	VAL	VAL	B	B	0 - 387	1 - 388
2	4	GLY	GLY	VAL	VAL	C	C	0 - 387	1 - 388
1	5	GLY	GLY	VAL	VAL	B	B	0 - 387	1 - 388
2	5	GLY	GLY	VAL	VAL	D	D	0 - 387	1 - 388
1	6	GLY	GLY	VAL	VAL	C	C	0 - 387	1 - 388
2	6	GLY	GLY	VAL	VAL	D	D	0 - 387	1 - 388
1	7	LEU	LEU	PHE	PHE	E	E	22 - 223	23 - 224
2	7	LEU	LEU	PHE	PHE	F	F	22 - 223	23 - 224
1	8	LEU	LEU	ILE	ILE	E	E	22 - 227	23 - 228
2	8	LEU	LEU	ILE	ILE	G	G	22 - 227	23 - 228
1	9	LEU	LEU	SER	SER	E	E	22 - 226	23 - 227
2	9	LEU	LEU	SER	SER	H	H	22 - 226	23 - 227
1	10	PHE	PHE	LYS	LYS	F	F	21 - 224	22 - 225
2	10	PHE	PHE	LYS	LYS	G	G	21 - 224	22 - 225
1	11	PHE	PHE	PHE	PHE	F	F	21 - 223	22 - 224
2	11	PHE	PHE	PHE	PHE	H	H	21 - 223	22 - 224
1	12	PHE	PHE	ASN	ASN	G	G	21 - 228	22 - 229
2	12	PHE	PHE	ASN	ASN	H	H	21 - 228	22 - 229

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12

#1: Protein

ATP phosphoribosyltransferase regulatory subunit

Mass: 43129.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Loops missing in model due to flexibility / Source: (gene. exp.)

Psychrobacter arcticus (bacteria) / Gene: hisZ, Psyc_0676 / Plasmid: pJexpress414 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4FTX3

#2: Protein

ATP phosphoribosyltransferase / ATP-PRTase

Mass: 25240.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Loops missing from model due to flexibility / Source: (gene. exp.)

Psychrobacter arcticus (bacteria) / Gene: hisG, Psyc_1903 / Plasmid: pJexpress431 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4FQF7, ATP phosphoribosyltransferase

#3: Chemical

ChemComp-HIS / HISTIDINE

Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₀N₃O₂

#4: Sugar

ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose

Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₅H₁₃O₁₄P₃

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.43 Å³/Da / Density % sol: 49.39 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 8mg mL-1 protein (in 20mM Tris pH7, 50mM KCl, 10mM MgCl2, 2mM DTT, 0.5mM histidine) mixed in 1:1 ratio with precipitant solution (11% PEG3350, 100mM bicine pH8.5, 150mM SrCl2, 150mM KBr, 2% 1,6-hexanediol)

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 0.9686 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9686 Å / Relative weight: 1

Reflection

Resolution: 2.65→77.31 Å / Num. obs: 75715 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.072 / R_pim(I) all: 0.047 / R_rim(I) all: 0.086 / Net I/σ(I): 6.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2.65-2.7	3.4	1.247	4488	0.456	0.794	1.482	99.8
13.25-77.31	2.9	0.03	610	0.996	0.021	0.037	95.4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R rigid body: 0.457

	Highest resolution	Lowest resolution
Rotation	77.31 Å	3.09 Å

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Processing

Software

Name	Version	Classification
REFMAC	refmac_5.8.0238	refinement
XDS		data reduction
Aimless	0.7.3	data scaling
MOLREP		phasing
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6FTT

6ftt

Resolution: 2.65→77.31 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.919 / Matrix type: sparse / SU B: 42.149 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.365
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2701	3726	4.9 %	RANDOM
R_work	0.2359	-	-	-
obs	0.2376	71962	99.84 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 175.02 Å² / B_iso mean: 75.679 Å² / B_iso min: 34.24 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.09 Å²	0 Å²	1.24 Å²
2-	-	-0.84 Å²	0 Å²
3-	-	-	0.15 Å²

Refinement step

Cycle: final / Resolution: 2.65→77.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17863	0	88	54	18005
B_iso mean	-	-	136.58	60.16	-
Num. residues	-	-	-	-	2330

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	18308
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	17161
X-RAY DIFFRACTION	r_angle_refined_deg	1.286	1.638	24878
X-RAY DIFFRACTION	r_angle_other_deg	1.114	1.573	39655
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.649	5	2313
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.689	22.468	932
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.104	15	3052
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.982	15	118
X-RAY DIFFRACTION	r_chiral_restr	0.043	0.2	2437
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	20489
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3673

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	11254	0.08
1	2	B	11254	0.08
2	1	A	11206	0.08
2	2	C	11206	0.08
3	1	A	11338	0.07
3	2	D	11338	0.07
4	1	B	11466	0.07
4	2	C	11466	0.07
5	1	B	11195	0.08
5	2	D	11195	0.08
6	1	C	11227	0.08
6	2	D	11227	0.08
7	1	E	5404	0.08
7	2	F	5404	0.08
8	1	E	5772	0.07
8	2	G	5772	0.07
9	1	E	5655	0.07
9	2	H	5655	0.07
10	1	F	5594	0.07
10	2	G	5594	0.07
11	1	F	5509	0.06
11	2	H	5509	0.06
12	1	G	5796	0.07
12	2	H	5796	0.07

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 (%)
2.65-2.719	0.386	249	0.388	5316	X-RAY DIFFRACTION	99.856
2.719-2.793	0.344	258	0.358	5200	X-RAY DIFFRACTION	99.927
2.793-2.874	0.356	266	0.328	4986	X-RAY DIFFRACTION	99.905
2.874-2.962	0.354	253	0.31	4903	X-RAY DIFFRACTION	99.884
2.962-3.06	0.312	217	0.292	4779	X-RAY DIFFRACTION	99.86
3.06-3.167	0.33	232	0.282	4584	X-RAY DIFFRACTION	99.855
3.167-3.286	0.312	222	0.261	4428	X-RAY DIFFRACTION	99.936
3.286-3.42	0.28	254	0.243	4235	X-RAY DIFFRACTION	99.978
3.42-3.572	0.258	206	0.226	4072	X-RAY DIFFRACTION	99.883
3.572-3.746	0.26	220	0.212	3890	X-RAY DIFFRACTION	99.976
3.746-3.949	0.256	175	0.219	3742	X-RAY DIFFRACTION	99.923
3.949-4.188	0.242	188	0.195	3506	X-RAY DIFFRACTION	99.838
4.188-4.476	0.208	181	0.182	3309	X-RAY DIFFRACTION	99.886
4.476-4.834	0.227	178	0.18	3051	X-RAY DIFFRACTION	100
4.834-5.294	0.221	167	0.185	2833	X-RAY DIFFRACTION	100
5.294-5.917	0.27	134	0.216	2580	X-RAY DIFFRACTION	100
5.917-6.828	0.283	104	0.231	2295	X-RAY DIFFRACTION	100
6.828-8.352	0.279	107	0.215	1923	X-RAY DIFFRACTION	99.803
8.352-11.768	0.249	73	0.221	1507	X-RAY DIFFRACTION	99.496

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	1.751	-0.0968	0.6344	1.6441	-0.373	0.9353	-0.1124	0.1718	0.4728	-0.1416	0.0299	0.0384	-0.1657	-0.0605	0.0826	0.1582	-0.0458	0.0439	0.119	0.1082	0.3309	12.752	11.065	7.042
2	1.582	-0.0817	0.4004	1.4251	-0.3515	1.149	0.0831	-0.2101	-0.1543	0.1196	-0.0653	-0.1742	0.1334	-0.0774	-0.0178	0.0915	-0.0391	0.0404	0.0538	0.0515	0.2163	22.431	-11.741	21.267
3	1.8199	0.1383	0.357	1.2687	0.0644	1.382	0.0597	0.191	-0.0685	-0.1931	-0.1007	0.1468	0.2283	0.0561	0.041	0.111	0.0324	0.0503	0.0366	-0.0311	0.2013	-33.599	-11.61	27.214
4	1.6846	-0.1163	0.5701	1.449	0.1481	1.4071	-0.1142	-0.3137	0.5805	0.1834	0.0115	-0.1006	-0.2457	0.1629	0.1027	0.1492	0.0011	0.0463	0.1597	-0.151	0.4168	-24.207	9.782	43.237
5	3.7549	-0.9024	-1.9749	1.8415	0.9475	2.873	-0.038	-0.6137	0.395	0.2256	0.02	-0.1807	-0.0919	0.3312	0.0179	0.2948	-0.1273	-0.0536	0.5266	-0.1617	0.483	9.377	12.501	58.581
6	5.3147	-0.7095	-1.5659	1.0084	0.6672	1.6187	-0.1353	-0.9013	-0.3919	0.2648	0.0449	0.037	0.2837	0.1229	0.0903	0.3821	0.0033	0.0841	0.6288	0.148	0.3191	13.549	-13.301	57.032
7	2.9454	0.6897	-1.7063	1.8356	-0.9285	2.281	0.0012	0.1938	0.2432	-0.2076	0.0371	0.1478	-0.0537	-0.1799	-0.0382	0.3032	0.0475	-0.0438	0.2417	0.1204	0.4439	-20.144	15.201	-8.801
8	5.9252	0.2633	-0.6949	1.3653	-0.0834	2.0859	-0.1728	0.5344	-0.2854	-0.2223	0.0541	-0.0379	0.2781	-0.181	0.1187	0.4026	-0.042	0.0591	0.3081	0.0132	0.2063	-24.924	-10.687	-8.433

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 401
2	X-RAY DIFFRACTION	2	B	0 - 401
3	X-RAY DIFFRACTION	3	C	0 - 401
4	X-RAY DIFFRACTION	4	D	0 - 401
5	X-RAY DIFFRACTION	5	E	21 - 227
6	X-RAY DIFFRACTION	6	F	21 - 226
7	X-RAY DIFFRACTION	7	G	21 - 228
8	X-RAY DIFFRACTION	8	H	21 - 228

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