PDB-4h9m: The first Jack bean urease (Canavalia ensiformis) complex obtaine...

ID or keywords:

Entry

Database: PDB / ID: 4h9m

Title

The first Jack bean urease (Canavalia ensiformis) complex obtained at 1.52 resolution

Components

Urease

Keywords

HYDROLASE / Jack bean / Canavalia ensiformis / acetohydroxamic acid / Metal-binding / Nickel

Function / homology

Function and homology information

urease complex / urease / urease activity / urea catabolic process / : / nickel cation binding / toxin activity
Similarity search - Function

Biological species

Canavalia ensiformis (jack bean)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.52 Å

Authors

Begum, A. / Choudhary, M.I. / Betzel, C.

Citation

Journal: TO BE PUBLISHED
Title: The first Jack bean urease (Canavalia ensiformis) complex obtained at 1.52 resolution
Authors: Begum, A. / Choudhary, M.I. / Betzel, C.

History

Deposition	Sep 24, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 24, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4h9m.cif.gz	348.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4h9m.ent.gz	283.1 KB	Display	PDB format
PDBx/mmJSON format	4h9m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4h9m_validation.pdf.gz	470.9 KB	Display	wwPDB validaton report
Full document	4h9m_full_validation.pdf.gz	477.9 KB	Display
Data in XML	4h9m_validation.xml.gz	41.3 KB	Display
Data in CIF	4h9m_validation.cif.gz	64.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h9/4h9m ftp://data.pdbj.org/pub/pdb/validation_reports/h9/4h9m	HTTPS FTP

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Related structure data

Related structure data	4gy7S S: Starting model for refinement
Similar structure data	4gy7-1 6zo2-1 5fse-1 4cex-1 6i9y-1 5fsd-1 5a6t-1 5g4h-1 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	#158 - Feb 2013 Proton-Gated Urea Channel similarity (21) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (4)

Deposited unit

A: Urease

hetero molecules

93.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Urease

hetero molecules

A: Urease

hetero molecules

A: Urease

hetero molecules

defined by author&software
280 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	140.391, 140.391, 198.747
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	182
Space group name H-M	P6₃22

Components on special symmetry positions

ID	Model	Components
1	1	A-1242- HOH
2	1	A-1462- HOH
3	1	A-1541- HOH
4	1	A-1543- HOH

#1: Protein	Urease / Urea amidohydrolase Mass: 91402.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: plant source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P07374, urease
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-HAE / ACETOHYDROXAMIC ACID Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₅NO₂ / Comment: inhibitor, medication*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 965 / 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: 3.09 Å³/Da / Density % sol: 60.22 %
Crystal grow	Temperature: 293 K / pH: 8.8 Details: 1.6M ammonium phosphate dibasic, 100mM Tris pH 8.8, 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 293 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 9, 2012 / Details: MIRRORS
Radiation	Monochromator: HORIZONTALLY FOCUSSING MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8123 Å / Relative weight: 1
Reflection	Resolution: 1.518→20 Å / Num. obs: 223658 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 7.5 % / R_merge(I) obs: 0.093
Reflection shell	Highest resolution: 1.52 Å / % possible all: 99.5

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Processing

Software

Name	Version	Classification
DNA		data collection
MOLREP		phasing
REFMAC	5.7.0029	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4GY7

4gy7

Resolution: 1.52→19.61 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.963 / SU B: 2.279 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.191	8814	5 %	RANDOM
R_work	0.178	-	-	-
obs	0.178	167228	99.6 %	-

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: 19.86 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.61 Å²	0.61 Å²	0 Å²
2-	-	0.61 Å²	0 Å²
3-	-	-	-1.98 Å²

Refinement step

Cycle: LAST / Resolution: 1.52→19.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6365	0	123	965	7453

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.019	6767
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.075	1.984	9150
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.681	5	896
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.828	24.353	278
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.321	15	1142
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.075	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	1041
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	5039
X-RAY DIFFRACTION	r_gen_planes_other
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_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.52→1.56 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	610	-
R_work	0.276	12041	-
obs	-	-	98.38 %

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	0.3956	0.1557	0.1508	0.4858	0.2723	0.618	-0.0142	-0.0643	0.0496	0.0079	-0.0064	0.0488	-0.0525	-0.0559	0.0206	0.0427	0.0144	0.0077	0.0459	0.0002	0.0506	-14.2336	-73.5617	-0.5057
2	1.7595	-0.6152	-0.0368	1.5452	0.582	1.919	-0.0341	-0.1468	0.0667	0.1744	0.0549	-0.0014	-0.059	-0.042	-0.0208	0.0742	0.0104	0.0184	0.0838	-0.0096	0.0648	-10.3218	-70.5266	12.3295
3	6.3634	-1.2824	3.1897	0.3031	-0.3066	4.1969	-0.4932	-0.5188	0.3444	0.1576	-0.0581	-0.0218	0.0112	-1.5716	0.5513	0.9105	0.0491	-0.109	0.7693	-0.1417	0.3433	-6.9866	-50.7115	4.7777
4	4.4245	-0.4762	2.4289	0.1943	-0.1827	1.5522	-0.162	-0.3396	0.3062	0.1041	0.0023	0.0482	-0.0784	-0.2156	0.1596	0.1154	0.0446	0.0317	0.102	-0.0369	0.1176	-24.9709	-44.0893	-14.122
5	1.3361	0.2422	0.1087	2.3218	-0.5176	0.2935	0.0255	0.0271	0.0492	0.06	0.0162	0.172	-0.0402	-0.0412	-0.0417	0.0725	0.0515	0.0231	0.1101	-0.0147	0.0897	-50.2015	-56.0741	-23.3031
6	0.8707	0.1603	-0.3011	0.8073	0.0631	0.3802	0.0401	0.0085	-0.0072	0.0181	-0.0247	0.029	-0.0347	-0.0565	-0.0153	0.0398	0.0526	0.0095	0.0801	-0.0059	0.0825	-45.6678	-56.6955	-28.4586
7	3.2946	2.0018	-0.5296	4.3743	-1.0436	3.8372	0.0184	0.17	0.0164	-0.0514	0.0219	0.2555	0.0299	-0.3294	-0.0402	0.0532	0.0738	-0.0034	0.1425	-0.0102	0.0879	-54.5905	-56.8604	-41.016
8	2.5459	0.5259	-0.1704	3.2501	0.979	0.9037	-0.0641	0.0976	0.2048	-0.161	-0.0027	0.3418	-0.0668	-0.128	0.0668	0.0562	0.0668	-0.009	0.1141	0.0184	0.0638	-54.8747	-51.1637	-28.9328
9	2.874	7.922	0.1432	24.0746	5.365	11.1721	0.1696	-0.2296	0.267	0.0007	-0.6595	0.8558	-1.1614	-0.0866	0.49	0.2294	0.0948	-0.1177	0.1751	-0.1004	0.449	-40.3824	-35.7789	-20.3179
10	1.6926	-0.0982	0.4136	0.1591	-0.0742	0.2934	-0.0221	-0.1042	0.1297	0.0523	-0.0065	0.0202	-0.0825	-0.0861	0.0286	0.0752	0.0406	0.0062	0.0468	-0.0237	0.0994	-21.9244	-45.7465	-17.2168
11	0.518	-0.0511	-0.0279	0.1004	0.0132	0.0994	0.0196	0.0258	0.0417	0.002	-0.0144	0.0139	-0.0537	-0.0256	-0.0052	0.0479	0.0158	0.0048	0.0465	-0.0025	0.0724	-11.2336	-59.0528	-30.8853
12	0.9199	0.6783	0.1252	1.0308	-0.0507	0.3958	-0.0339	0.0636	-0.0731	-0.0081	0.0298	-0.059	-0.0133	0.0464	0.0041	0.03	-0.0061	-0.0036	0.0436	-0.0017	0.0544	12.1676	-67.0053	-36.44
13	0.3022	-0.0214	-0.0044	0.2362	0.0254	0.2224	-0.0054	0.0061	0.0393	0.009	0.0053	-0.0129	-0.0549	0.0349	0	0.0455	-0.0361	-0.0075	0.0462	0.0018	0.0855	21.148	-51.288	-29.1739
14	2.5267	-0.2417	-0.6091	2.1498	0.352	0.5125	-0.0631	-0.1528	-0.2222	0.156	-0.0254	-0.2658	0.0347	0.1123	0.0885	0.0654	-0.0327	-0.0246	0.1047	0.0135	0.1085	28.7232	-56.0841	-10.6766
15	0.5241	0.1297	0.0416	0.0868	-0.0898	0.1877	0.0099	-0.055	0.055	0.0434	-0.0157	0.0104	-0.0774	0.0039	0.0058	0.0443	-0.015	-0.0031	0.019	-0.0144	0.0584	7.8356	-50.1486	-16.9987
16	6.3154	0.45	3.3829	1.5668	1.0267	3.9082	-0.2612	-0.2008	0.7218	-0.0187	0.0828	0.0132	-0.5924	-0.025	0.1784	0.1746	0.021	0.0006	0.0374	-0.0385	0.189	-3.5427	-37.5684	-16.7041
17	0.2072	0.0603	-0.0372	0.1201	-0.0356	0.2103	-0.0111	0.0041	0.0224	0.0024	0.011	0.0102	-0.0122	-0.0375	0	0.0415	0.0109	0.002	0.0463	-0.0037	0.0734	-6.4974	-59.7939	-24.9111
18	0.2916	0.0927	-0.1037	0.3522	0.0596	0.423	-0.0283	0.0595	0.0107	-0.0326	0.032	-0.0117	-0.0206	-0.0021	-0.0037	0.0478	-0.0021	-0.0117	0.0635	0.0037	0.0792	3.8234	-60.3598	-38.2611
19	9.3727	-4.9642	5.3492	6.7169	-2.6138	6.6317	-0.2774	-0.3397	0.1816	0.3198	0.2395	0.0182	-0.4723	-0.1661	0.0378	0.1127	-0.0447	-0.0047	0.0652	-0.0283	0.1491	21.6624	-35.6608	-15.5837
20	1.5325	0.4904	0.0549	1.9675	0.0479	1.0066	0.0076	-0.0671	0.1344	0.0806	-0.0459	-0.0597	-0.154	0.1521	0.0383	0.0797	-0.0028	-0.0024	0.0779	-0.0088	0.0683	3.0894	-54.5536	-5.821

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 101
2	X-RAY DIFFRACTION	2	A	102 - 124
3	X-RAY DIFFRACTION	3	A	125 - 132
4	X-RAY DIFFRACTION	4	A	133 - 148
5	X-RAY DIFFRACTION	5	A	149 - 164
6	X-RAY DIFFRACTION	6	A	165 - 232
7	X-RAY DIFFRACTION	7	A	233 - 246
8	X-RAY DIFFRACTION	8	A	247 - 262
9	X-RAY DIFFRACTION	9	A	263 - 268
10	X-RAY DIFFRACTION	10	A	269 - 306
11	X-RAY DIFFRACTION	11	A	307 - 450
12	X-RAY DIFFRACTION	12	A	451 - 474
13	X-RAY DIFFRACTION	13	A	475 - 587
14	X-RAY DIFFRACTION	14	A	588 - 613
15	X-RAY DIFFRACTION	15	A	614 - 656
16	X-RAY DIFFRACTION	16	A	657 - 674
17	X-RAY DIFFRACTION	17	A	675 - 744
18	X-RAY DIFFRACTION	18	A	745 - 805
19	X-RAY DIFFRACTION	19	A	806 - 823
20	X-RAY DIFFRACTION	20	A	824 - 840

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