PDB-4rhm: Crystal structure of T. brucei arginase-like protein quadruple mu...

ID or keywords:

Entry

Database: PDB / ID: 4rhm

Title

Crystal structure of T. brucei arginase-like protein quadruple mutant S149D/R151H/S153D/S226D

Components

Arginase

Keywords

UNKNOWN FUNCTION / arginase-deacetylase fold

Function / homology

Function and homology information

putrescine biosynthetic process from arginine, via agmatine / agmatinase activity / arginine metabolic process / arginase / arginase activity / metal ion binding
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / PHASER / Resolution: 1.95 Å

Authors

Hai, Y. / Barrett, M.P. / Christianson, D.W.

Citation

Journal: Biochemistry / Year: 2015
Title: Crystal Structure of an Arginase-like Protein from Trypanosoma brucei That Evolved without a Binuclear Manganese Cluster.
Authors: Hai, Y. / Kerkhoven, E.J. / Barrett, M.P. / Christianson, D.W.

History

Deposition	Oct 2, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 31, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 14, 2015	Group: Database references
Revision 1.2	Feb 4, 2015	Group: Database references
Revision 1.3	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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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	4rhm.cif.gz	363.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4rhm.ent.gz	297.2 KB	Display	PDB format
PDBx/mmJSON format	4rhm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4rhm_validation.pdf.gz	478 KB	Display	wwPDB validaton report
Full document	4rhm_full_validation.pdf.gz	488.5 KB	Display
Data in XML	4rhm_validation.xml.gz	34.5 KB	Display
Data in CIF	4rhm_validation.cif.gz	47 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rh/4rhm ftp://data.pdbj.org/pub/pdb/validation_reports/rh/4rhm	HTTPS FTP

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Related structure data

Related structure data	4rhiC 4rhjC 4rhkSC 4rhlC 4rhqC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4rhq-d 4rhj-2 3er8-1 1jcm-2 1lrn-1 4rhj-4 5tnv-1 1pbn-1 2ef9-1 4h41-d 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

Deposited unit

A: Arginase

B: Arginase

C: Arginase

hetero molecules

117 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	82.123, 137.350, 87.778
Angle α, β, γ (deg.)	90.00, 102.28, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-526- HOH

#1: Protein	Arginase Mass: 38797.230 Da / Num. of mol.: 3 / Mutation: S149D, R151H, S153D, S226D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.8.2020 / Production host: Escherichia coli (E. coli) / References: UniProt: Q581Y0, arginase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.08 Å³/Da / Density % sol: 40.81 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M KNO3, 20% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2014

Radiation

Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. all: 68553 / Num. obs: 64646 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / B_iso Wilson estimate: 29.9 Å² / R_merge(I) obs: 0.091 / R_sym value: 0.091 / Net I/σ(I): 17.1

Reflection shell

Resolution (Å)	Diffraction-ID	% possible all
1.95-2.01	1	73.4
2.01-2.08	1	80.9
2.08-2.17	1	88.4
2.17-2.27	1	96.1
2.27-2.39	1	99.4
2.39-2.54	1	99.6
2.54-2.73	1	99.7
2.73-3.01	1	99.9
3.01-3.44	1	100
3.44-4.34	1	100
4.34-50	1	99.8

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Processing

Software

Name	Version	Classification
CBASS		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.3_1479)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure: PHASER
Starting model: PDB ENTRY 4RHK

4rhk

Resolution: 1.95→42.88 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 32.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.237	3247	5.03 %
R_work	0.201	-	-
obs	0.203	64546	94 %
all	-	64646	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→42.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7076	0	51	129	7256

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7289
X-RAY DIFFRACTION	f_angle_d	0.778	9874
X-RAY DIFFRACTION	f_dihedral_angle_d	12.56	2707
X-RAY DIFFRACTION	f_chiral_restr	0.03	1096
X-RAY DIFFRACTION	f_plane_restr	0.004	1275

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 (%)
1.95-1.9826	0.3466	107	0.3161	1920	X-RAY DIFFRACTION	69
1.9826-2.0136	0.3324	121	0.3098	2086	X-RAY DIFFRACTION	74
2.0136-2.0466	0.3753	117	0.3	2273	X-RAY DIFFRACTION	79
2.0466-2.0819	0.3498	119	0.2892	2300	X-RAY DIFFRACTION	82
2.0819-2.1197	0.3254	122	0.2848	2408	X-RAY DIFFRACTION	85
2.1197-2.1605	0.3278	134	0.2816	2514	X-RAY DIFFRACTION	89
2.1605-2.2046	0.2978	155	0.2857	2598	X-RAY DIFFRACTION	93
2.2046-2.2525	0.3188	130	0.271	2735	X-RAY DIFFRACTION	96
2.2525-2.3049	0.3391	147	0.2499	2793	X-RAY DIFFRACTION	99
2.3049-2.3626	0.2731	140	0.2398	2834	X-RAY DIFFRACTION	99
2.3626-2.4264	0.2493	157	0.2271	2815	X-RAY DIFFRACTION	99
2.4264-2.4978	0.2374	129	0.2285	2835	X-RAY DIFFRACTION	99
2.4978-2.5785	0.3005	133	0.2305	2820	X-RAY DIFFRACTION	100
2.5785-2.6706	0.2862	153	0.223	2830	X-RAY DIFFRACTION	99
2.6706-2.7775	0.2624	158	0.2136	2789	X-RAY DIFFRACTION	100
2.7775-2.9039	0.2654	162	0.22	2822	X-RAY DIFFRACTION	100
2.9039-3.0569	0.2888	157	0.21	2828	X-RAY DIFFRACTION	100
3.0569-3.2484	0.2556	146	0.2046	2820	X-RAY DIFFRACTION	100
3.2484-3.4991	0.2244	156	0.1984	2852	X-RAY DIFFRACTION	100
3.4991-3.851	0.2028	156	0.185	2821	X-RAY DIFFRACTION	100
3.851-4.4078	0.2231	128	0.1629	2881	X-RAY DIFFRACTION	100
4.4078-5.5515	0.176	154	0.1536	2847	X-RAY DIFFRACTION	100
5.5515-42.8958	0.1748	166	0.164	2878	X-RAY DIFFRACTION	100

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	0.2521	-0.0828	0.2037	0.5534	-0.2427	-0.1252	-0.0366	-0.1579	0.117	0.0685	0.0386	-0.0482	-0.0439	-0.0252	0	0.333	0.0518	0.0535	0.2894	0.005	0.3773	21.986	27.511	24.2212
2	0.011	-0.1497	-0.0519	0.7428	-0.0569	-0.0063	0.0687	-0.0248	0.0595	-0.1769	0.0349	0.0805	0.0002	-0.0059	0	0.2482	0.0149	-0.0313	0.2114	0.0432	0.1162	20.3358	12.3294	13.5118
3	0.0193	-0.0503	0.0005	0.1588	-0.0127	0.0039	0.0858	-0.0614	-0.0095	0.0019	0.0464	-0.0118	0.0485	-0.0212	0.0002	0.9624	-0.097	-0.0969	0.9122	0.1801	0.611	32.8456	20.5346	-1.9366
4	0.1783	0.0212	-0.0803	0.0849	0.0248	0.0143	-0.0966	-0.0191	-0.2086	0.2921	-0.1933	0.3437	-0.0556	-0.0332	-0	0.4658	-0.0832	0.0737	0.3772	0.0746	0.459	10.5896	-31.7919	26.0579
5	0.1924	0.0785	0.0524	0.2974	0.1333	0.0594	-0.0742	-0.0048	0.0503	0.0276	-0.0109	0.1301	-0.0319	-0.0152	0	0.327	-0.0353	-0.0286	0.3152	-0.0121	0.3512	12.5608	-17.7394	17.2673
6	-0.0016	0.0324	-0.0077	0.0427	-0.0007	0.0233	0.0205	-0.1128	-0.4037	0.0275	-0.0396	0.0886	0.0222	-0.1148	0	0.4479	-0.08	0.003	0.3802	0.053	0.6084	18.3164	-31.0694	29.2405
7	0.0003	0.0129	-0.0449	-0.0105	0.0213	-0.0043	-0.1446	-0.1012	-0.1954	0.1046	-0.0641	-0.009	-0.1375	-0.0004	-0	0.3234	-0.0386	-0.0355	0.2573	0.0044	0.4377	23.1355	-30.0524	18.8565
8	0.0111	-0.0131	-0.0413	-0.0175	0.031	-0.0893	-0.0879	-0.0644	-0.1726	0.0102	0.0241	-0.0826	-0.0131	-0.0195	-0	0.2585	0.02	0.0063	0.2328	-0.0385	0.3585	38.368	-27.5151	16.9525
9	0.0238	0.0112	0.0337	0.0164	-0.0091	0.006	-0.0192	0.0761	-0.0258	-0.06	0.3481	-0.1467	-0.0952	0.0489	0	0.4731	0.0109	0.0876	0.3653	-0.0471	0.3238	41.4995	-14.5813	9.9485
10	0.0149	-0.053	-0.0002	0.0259	-0.0111	0.0004	0.0762	-0.0671	-0.5152	-0.0522	0.168	-0.437	-0.0316	-0.0381	0	0.2925	-0.0332	0.0311	0.234	-0.1198	0.2468	31.002	-19.9298	9.7815
11	0.1114	0.1596	-0.1005	0.0732	0.0553	0.0216	-0.0075	-0.0368	-0.1166	-0.0365	0.035	-0.078	0.0112	-0.0327	-0	0.2746	0.0081	-0.0134	0.2608	0.0118	0.1706	28.7133	-11.7846	22.0143
12	0.0736	0.077	0.0028	-0.0118	-0.0174	0.024	-0.2448	0.0362	-0.1462	-0.1523	0.2606	0.0687	-0.3501	0.0984	-0	0.2284	-0.0698	-0.0487	0.2692	-0.0061	0.239	21.7763	-14.2571	12.8585
13	0.1995	0.0959	0.2638	0.1892	-0.1919	0.1588	0.1848	-0.2852	-0.0602	0.0714	0.0156	-0.1335	0.072	0.0853	-0	0.2578	0.0547	-0.067	0.4494	-0.1111	0.406	60.4383	-4.2106	37.3406
14	0.3292	0.0839	-0.264	0.3842	-0.1239	0.0121	0.0338	-0.2641	-0.1421	-0.0511	-0.0103	-0.2001	0.0698	0.0138	0	0.2494	0.0178	-0.056	0.4736	-0.0858	0.5293	60.3884	-6.4301	33.8155
15	0.1526	-0.3134	-0.1256	0.2328	0.1322	-0.0514	0.0179	-0.0943	0.0758	-0.1775	0.0795	-0.3032	-0.0952	-0.0609	0	0.2259	-0.046	0.0861	0.2412	-0.0584	0.4585	56.046	12.1461	22.0783
16	0.2629	-0.096	0.0768	0.1857	0.0949	0.0214	0.0132	-0.0457	0.0753	-0.0262	0.0659	-0.2822	-0.0016	-0.028	0	0.1864	0.0098	0.0296	0.2081	-0.0345	0.2165	48.7314	0.1987	24.2227

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID -1:112 )	A	-1 - 112
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 113:304 )	A	113 - 304
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 305:306 )	A	305 - 306
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID -1:16 )	B	-1 - 16
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 17:80 )	B	17 - 80
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 81:113 )	B	81 - 113
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 114:137 )	B	114 - 137
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 138:191 )	B	138 - 191
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 192:209 )	B	192 - 209
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 210:227 )	B	210 - 227
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 228:282 )	B	228 - 282
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 283:306 )	B	283 - 306
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID -1:47 )	C	-1 - 47
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 48:113 )	C	48 - 113
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 114:209 )	C	114 - 209
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 210:304 )	C	210 - 304

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