PDB-4brp: Legionella pneumophila NTPDase1 crystal form V (part-open)

ID or keywords:

Entry

Database: PDB / ID: 4brp

Title

Legionella pneumophila NTPDase1 crystal form V (part-open)

Components

ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

Keywords

HYDROLASE / APYRASE / ATPASE / ADPASE / CD39 / PURINERGIC SIGNALLING / DOMAIN ROTATION / TRANSITION STATE / NTPDASE

Function / homology

Function and homology information

nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / nucleotide binding / metal ion binding / membrane
Similarity search - Function

Biological species

LEGIONELLA PNEUMOPHILA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Zebisch, M. / Schaefer, P. / Lauble, P. / Straeter, N.

Citation

Journal: Structure / Year: 2013
Title: Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases
Authors: Zebisch, M. / Krauss, M. / Schaefer, P. / Lauble, P. / Straeter, N.

History

Deposition	Jun 4, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 17, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2013	Group: Database references
Revision 1.2	Dec 25, 2013	Group: Structure summary
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4brp.cif.gz	563 KB	Display	PDBx/mmCIF format
PDB format	pdb4brp.ent.gz	468.4 KB	Display	PDB format
PDBx/mmJSON format	4brp.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4brp_validation.pdf.gz	457.5 KB	Display	wwPDB validaton report
Full document	4brp_full_validation.pdf.gz	463.7 KB	Display
Data in XML	4brp_validation.xml.gz	53.4 KB	Display
Data in CIF	4brp_validation.cif.gz	69.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/br/4brp ftp://data.pdbj.org/pub/pdb/validation_reports/br/4brp	HTTPS FTP

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Related structure data

Related structure data	4bqzC 4br0C 4br2C 4br4C 4br5C 4br7C 4br9C 4braC 4brcC 4brdC 4breC 4brfC 4brgC 4brhC 4briC 4brkC 4brlC 4brmC 4brnC 4broC 4brqC C: citing same article (ref.)
Similar structure data	3maf-d 6tb0-d 3ei5-d 3eia-d 4brn-d 6g4b-d 2z20-d 3ei7-d 5ykr-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

C: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

D: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

hetero molecules

168 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

D: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

hetero molecules

defined by author&software
84 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

B: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

hetero molecules

defined by author&software
84.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	129.608, 129.608, 162.698
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 38 - 391 / Label seq-ID: 5 - 358

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	B	B
2	4	C	C
1	5	B	B
2	5	D	D
1	6	C	C
2	6	D	D

NCS ensembles :

ID
1
2
3
4
5
6

NCS oper:

ID	Code	Matrix	Vector
1	given	(-1, 0.002, 0.003), (-0.002, -0.988, -0.151), (0.003, -0.151, 0.988)	62.687, -107.834, -8.374
2	given	(-0.999, -0.004, 0.033), (-0.033, 0.188, -0.982), (-0.002, -0.982, -0.188)	29.23, -20.074, -22.624
3	given	(1, -0.001, -0.031), (0.031, -0.003, 1), (-0.001, -1, -0.003)	33.409, -83.631, -28.752

#1: Protein	ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I / NTPDASE1 Mass: 41880.594 Da / Num. of mol.: 4 / Fragment: RESIDUES 35-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5ZUA2, apyrase
#2: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.4 Å³/Da / Density % sol: 48 % / Description: NONE
Crystal grow	pH: 6.4 / Details: 100MM NAMES PH 6.4, 14% PEG3350, 200MM KBR

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.2 / Wavelength: 0.9181

Radiation

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

Radiation wavelength

Wavelength: 0.9181 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.889
1	1	-h,-k,l	2	0.111

Reflection

Resolution: 2.5→29 Å / Num. obs: 55117 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / B_iso Wilson estimate: 66 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 11.8

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Processing

Software

Name: REFMAC / Version: 5.7.0029 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→29.08 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.938 / SU B: 16.069 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21866	1397	2.5 %	RANDOM
R_work	0.17711	-	-	-
obs	0.17814	53677	99.85 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 60.578 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-16.94 Å²	0 Å²	0 Å²
2-	-	-16.94 Å²	0 Å²
3-	-	-	33.88 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→29.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11065	0	7	14	11086

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	11402
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	10237
X-RAY DIFFRACTION	r_angle_refined_deg	1.82	1.934	15585
X-RAY DIFFRACTION	r_angle_other_deg	1.297	3.002	23504
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.396	5	1412
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.661	25.766	555
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.634	15	1738
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.117	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	1687
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	13316
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	2720
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.87

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	3054	3.4
1	2	B	3054	3.4
2	1	A	3092	3.85
2	2	C	3092	3.85
3	1	A	3027	3.9
3	2	D	3027	3.9

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.324	91	-
R_work	0.218	3902	-
obs	-	-	99.68 %

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	3.558	-1.1543	-0.0584	1.9868	0.0756	1.5328	0.1245	-0.1397	0.1277	-0.0507	-0.0805	-0.0666	-0.0542	-0.0141	-0.044	0.0781	0.0122	0.0347	0.2129	0.0281	0.0206	49.8317	-49.1243	13.4783
2	5.4716	-1.7229	-1.3409	4.7981	0.9942	2.452	0.2234	0.1422	0.0227	-0.2535	-0.0743	-0.4184	0.2113	0.3303	-0.1491	0.2382	0.0489	0.0602	0.4093	0.0518	0.0734	59.1234	-54.522	-1.0199
3	4.0533	0.3523	-0.028	1.2182	0.1676	1.1039	0.0879	0.4189	-0.1564	-0.3045	-0.1023	-0.0822	-0.042	0.1196	0.0144	0.326	0.2069	0.0448	0.3221	0.0291	0.0157	44.547	-61.3353	-11.8671
4	3.7672	-1.4048	0.1658	2.26	-0.5807	3.188	0.0262	-0.0734	-0.1495	-0.0435	0.0063	0.1468	-0.1023	-0.4714	-0.0325	0.104	0.0985	-0.0501	0.2798	-0.0311	0.0336	13.2618	-61.3219	12.7815
5	2.112	-1.9963	0.621	3.4376	-1.6228	7.6267	0.2612	0.1351	-0.1357	0.0839	0.0059	0.3508	-0.7144	-0.5355	-0.2671	0.3046	0.2552	-0.0391	0.5625	-0.0316	0.1082	4.7763	-53.3225	-0.2845
6	4.052	0.287	0.0458	1.132	0.0023	1.7934	0.1245	0.2742	0.2876	-0.2351	-0.1932	0.0914	-0.2292	-0.2763	0.0687	0.4109	0.3204	-0.0817	0.3942	0.0208	0.0815	18.026	-45.5052	-10.5897
7	9.1465	0.8773	-1.2555	2.9239	0.3796	1.6926	-0.6225	1.2941	-0.5433	-0.2713	0.36	-0.1508	0.2195	0.0609	0.2625	0.1234	-0.0804	0.0563	0.5282	0.0075	0.0827	-19.5315	-41.0684	22.4008
8	8.1592	1.7963	0.7706	4.9894	-0.2372	4.2494	-0.3636	0.4069	1.0968	0.3182	0.0239	0.5966	0.3499	-0.3169	0.3396	0.1437	-0.028	-0.0505	0.2731	0.1415	0.3802	-29.1197	-27.4284	30.3954
9	3.7359	1.0708	1.1867	1.1849	0.153	1.8962	-0.2104	0.0515	0.9841	0.0415	0.0397	0.5328	-0.1789	-0.1425	0.1707	0.0771	0.0367	-0.0507	0.1508	0.0794	0.4123	-13.742	-18.3961	39.2639
10	4.3107	1.1191	-1.1147	1.8263	-0.1418	1.5456	-0.1703	0.0419	-0.3171	-0.0436	0.0856	-0.0503	0.0939	0.1598	0.0847	0.0701	-0.0142	0.0103	0.2725	-0.0304	0.0277	17.5838	-42.4022	33.9504
11	5.5925	0.1416	-0.1154	7.9021	0.7316	0.8894	-0.268	0.4254	0.04	-0.7851	0.2208	-0.2063	0.2153	0.4005	0.0473	0.2587	-0.0479	0.0401	0.5002	0.0327	0.015	26.5118	-27.7611	28.4849
12	3.6884	1.3888	0.2651	1.2174	0.0115	0.9691	-0.2892	1.0275	0.7873	-0.3346	0.3808	0.1927	-0.0823	0.1163	-0.0916	0.1713	-0.1705	-0.057	0.5623	0.2985	0.2455	12.3754	-16.7912	22.8506

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	34 - 155
2	X-RAY DIFFRACTION	2	A	156 - 179
3	X-RAY DIFFRACTION	2	A	377 - 394
4	X-RAY DIFFRACTION	3	A	180 - 376
5	X-RAY DIFFRACTION	4	B	34 - 155
6	X-RAY DIFFRACTION	5	B	156 - 179
7	X-RAY DIFFRACTION	5	B	377 - 394
8	X-RAY DIFFRACTION	6	B	180 - 376
9	X-RAY DIFFRACTION	7	C	34 - 155
10	X-RAY DIFFRACTION	8	C	156 - 179
11	X-RAY DIFFRACTION	8	C	377 - 394
12	X-RAY DIFFRACTION	9	C	180 - 376
13	X-RAY DIFFRACTION	10	D	34 - 155
14	X-RAY DIFFRACTION	11	D	156 - 179
15	X-RAY DIFFRACTION	11	D	377 - 394
16	X-RAY DIFFRACTION	12	D	180 - 376

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