PDB-8d27: Arginase Domain of Ornithine Decarboxylase/Arginase from Fusobact...

ID or keywords:

Entry

Database: PDB / ID: 8d27

Title

Arginase Domain of Ornithine Decarboxylase/Arginase from Fusobacterium nucleatum

Components

Arginase

Keywords

HYDROLASE / arginase domain / ornithine decarboxylase/arginase / inactive / ODA

Function / homology

Function and homology information

arginine metabolic process / arginase / arginase activity / lyase activity / metal ion binding
Similarity search - Function

Biological species

Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.25 Å

Authors

Chan, A.C. / Kolesnikov, M. / Murphy, M.E.

Funding support

Canada, 1items

Citation

Journal: Biochemistry / Year: 2022
Title: Sequence Divergence in the Arginase Domain of Ornithine Decarboxylase/Arginase in Fusobacteriacea Leads to Loss of Function in Oral Associated Species.
Authors: Mothersole, R.G. / Kolesnikov, M. / Chan, A.C.K. / Oduro, E. / Murphy, M.E.P. / Wolthers, K.R.

History

Deposition	May 27, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Feb 14, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8d27.cif.gz	305.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8d27.ent.gz	254.9 KB	Display	PDB format
PDBx/mmJSON format	8d27.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8d27_validation.pdf.gz	428 KB	Display	wwPDB validaton report
Full document	8d27_full_validation.pdf.gz	430.3 KB	Display
Data in XML	8d27_validation.xml.gz	20.8 KB	Display
Data in CIF	8d27_validation.cif.gz	28.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d2/8d27 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/8d27	HTTPS FTP

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Related structure data

Similar structure data	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

64.2 kDa, 2 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)	44.818, 78.217, 73.530
Angle α, β, γ (deg.)	90.000, 90.030, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Arginase Mass: 32081.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria) Strain: ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355 Gene: FN0501 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q8RG18
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Arginase

Mass: 32081.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Strain: ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355
Gene: FN0501 / Plasmid: pET15b / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q8RG18

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.01 Å³/Da / Density % sol: 38.76 % / Mosaicity: 1.24 ° / Mosaicity esd: 0.012 °
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.07 M sodium acetate pH 4.6, 12% PEG 4000 and 25% glycerol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08B1-1 / Wavelength: 0.97946 Å

Detector

Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 31, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.97946 Å / Relative weight: 1

Reflection twin

Operator: h,-k,-l / Fraction: 0.45

Reflection

Resolution: 2.25→50 Å / Num. obs: 23357 / % possible obs: 97.4 % / Redundancy: 3.5 % / R_merge(I) obs: 0.146 / R_pim(I) all: 0.089 / R_rim(I) all: 0.171 / Χ²: 1.055 / Net I/σ(I): 6 / Num. measured all: 81549

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	Χ²	% possible all
2.25-2.29	2.9	0.488	998	0.663	0.323	0.587	0.776	83.8
2.29-2.33	3	0.44	1050	0.731	0.288	0.528	0.759	88.1
2.33-2.38	3	0.461	1101	0.753	0.303	0.553	0.822	92.1
2.38-2.42	3.2	0.459	1120	0.716	0.298	0.549	0.774	94.7
2.42-2.48	3.3	0.427	1165	0.748	0.274	0.508	0.844	97.1
2.48-2.53	3.4	0.4	1174	0.807	0.249	0.472	0.878	98.7
2.53-2.6	3.5	0.377	1178	0.84	0.232	0.443	0.89	99.7
2.6-2.67	3.6	0.38	1178	0.851	0.231	0.446	0.92	99.2
2.67-2.75	3.6	0.312	1192	0.884	0.19	0.366	0.896	99.4
2.75-2.83	3.6	0.293	1189	0.913	0.177	0.343	0.995	99.3
2.83-2.94	3.6	0.263	1190	0.915	0.159	0.308	1.094	99.7
2.94-3.05	3.6	0.21	1203	0.93	0.127	0.246	1.076	99.6
3.05-3.19	3.6	0.179	1198	0.951	0.108	0.21	1.27	99.6
3.19-3.36	3.6	0.156	1170	0.956	0.094	0.182	1.34	99.7
3.36-3.57	3.6	0.13	1204	0.964	0.079	0.152	1.257	99.3
3.57-3.85	3.7	0.117	1186	0.966	0.07	0.136	1.307	99.4
3.85-4.23	3.8	0.105	1193	0.976	0.063	0.123	1.34	99.6
4.23-4.85	3.8	0.089	1220	0.975	0.053	0.104	1.222	100
4.85-6.1	3.8	0.089	1225	0.978	0.053	0.104	1.091	100
6.1-50	3.7	0.075	1223	0.988	0.045	0.087	1.109	99

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R rigid body: 0.5

	Highest resolution	Lowest resolution
Rotation	44.82 Å	2.36 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2-4158	refinement
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.25→44.82 Å / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.46 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2123	1072	4.59 %
R_work	0.1805	22284	-
obs	0.1944	23341	96.95 %

Solvent computation

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

Displacement parameters

B_iso max: 73.02 Å² / B_iso mean: 34.9491 Å² / B_iso min: 14.97 Å²

Refinement step

Cycle: final / Resolution: 2.25→44.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4370	0	0	77	4447
B_iso mean	-	-	-	28.74	-
Num. residues	-	-	-	-	562

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 8

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.25-2.36	0.2543	123	0.2514	2372	2495	80
2.36-2.48	0.2891	165	0.2411	2683	2848	89
2.48-2.64	0.2512	139	0.24	2838	2977	94
2.64-2.84	0.2677	137	0.2234	2827	2964	95
2.84-3.13	0.2524	154	0.2126	2833	2987	95
3.13-3.58	0.2274	96	0.1911	2895	2991	96
3.58-4.51	0.1911	114	0.1623	2919	3033	96
4.51-44.82	0.1871	129	0.1629	2917	3046	95

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	-0.0002	0.0002	-0.0004	0.0027	-0.004	0.0055	0.0056	0.0068	0.0002	-0.016	-0.0035	0.001	0.0106	-0.0055	-0.0096	0.1521	0.0083	0.0016	0.3435	0.0152	0.0701	20.097	33.8906	55.8443
2	0.0016	-0.0009	-0.003	0.0038	0.0045	0.008	-0.008	-0.0012	-0.0024	0.0025	-0.0034	0.0052	0.0297	-0.0193	-0.0465	0.1466	0.0107	0.0129	0.3809	-0.0215	0.0844	16.439	37.8689	67.7651
3	-0.0002	0.0002	0.0001	0.0008	0.0001	0.0002	0.003	-0.0082	0.0002	0.0047	0.0049	0.0003	-0.0246	-0.0054	0.0167	0.2249	0.0048	0.0034	0.3922	-0.0186	0.0896	17.3558	45.5447	75.3159
4	0.0141	0.0043	-0.0036	0.0013	-0.0007	0.0055	-0.0041	0.0111	-0.0007	0.0038	-0.0129	0.0027	-0.0013	0.0037	-0.0348	0.2026	-0.016	0.0118	0.3327	-0.012	0.0801	28.7155	42.1776	78.4597
5	0.0052	0.0035	0.0048	0.005	0.0036	0.0094	0.0132	0.0032	0.0006	0.0108	-0.0001	-0.0023	-0.0021	0.0069	0.0163	0.2431	-0.0455	0.0061	0.3868	-0.0067	0.0957	33.0885	47.8611	68.0684
6	0.0009	-0.0002	-0.0033	0	0.0006	0.0121	-0.001	0.0152	0.0028	-0.0221	0.0078	-0.0012	-0.0169	-0.0049	0.0053	0.2389	-0.0007	0.006	0.3298	0.0083	0.0743	33.1164	40.0907	61.8854
7	0.0037	-0.0034	-0.0025	0.0052	0.001	0.0044	-0.001	0.0041	-0.0024	0.0083	-0.0061	0.0014	-0.0004	0.001	-0.0102	0.255	-0.0058	0.0115	0.3714	0.014	0.0938	12.6876	39.9671	37.6576
8	0.0085	-0.0019	0.0037	0.0004	-0.0008	0.0017	-0.0106	-0.0018	0.0004	0.0016	-0.0001	-0.0031	-0.0017	0.0104	-0.0204	0.2429	0.0158	-0.0085	0.3176	0.0087	0.0753	4.1044	34.3174	39.5606
9	0.002	0.0011	0.0044	0.0006	0.0025	0.0102	-0.0042	-0.0126	0.0017	0.0266	0.0014	-0.0036	-0.0059	0.0045	-0.0145	0.2316	0.015	-0.0118	0.3534	0.0026	0.0824	23.9506	38.2632	34.7981
10	0.0006	0.0005	0.0014	0.0006	-0.0001	0.007	-0.0013	0.0002	0.0002	-0.0016	-0.0011	0.0012	0.0078	-0.0036	-0.0029	0.2049	0.0119	0.0021	0.3087	-0.0125	0.0744	12.3895	38.8188	27.002
11	0.0031	0.0002	-0.0008	0.0014	0.0025	0.0058	-0.0103	-0.0041	-0.0019	0.0003	-0.0091	-0	-0.0057	-0.0076	-0.0438	0.2072	-0.023	0.001	0.2988	0.0054	0.0671	20.7575	50.1788	28.4682
12	0.0106	0.0033	0.0078	0.0052	0.0052	0.0074	0.0002	0.0011	0.0034	-0.0119	0.0142	0.0048	-0.0072	-0.025	0.0037	0.2692	0.0224	0.0176	0.3936	0.0021	0.0974	18.648	48.0072	20.722
13	0.0008	0.0015	0.0014	0.0027	0.0027	0.0027	0.01	0.0208	0.0034	0.0068	-0.0038	0.003	-0.0093	-0.0106	-0.0001	0.2509	-0.0041	0.0278	0.3903	0.0133	0.0937	9.2043	58.1032	23.8429
14	0.037	0.0006	-0.0123	0.002	-0.0034	0.01	-0.0116	0.0249	-0.0094	-0.0102	0.0024	0.0021	0.0019	-0.0055	-0.0017	0.2399	-0.0199	-0.0077	0.3843	0.0111	0.0935	0.1182	53.0375	31.6156
15	0.0062	-0.0038	-0.0005	0.003	0.0018	0.0038	-0.0125	-0.01	0.0026	0.0107	0.0137	-0.0033	-0.0094	0.0086	0.0127	0.2646	0.0074	-0.0137	0.3593	0.0119	0.0867	1.5066	43.6432	33.7887

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 501 through 576 )	A	501 - 576
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 577 through 642 )	A	577 - 642
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 643 through 687 )	A	643 - 687
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 688 through 714 )	A	688 - 714
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 715 through 746 )	A	715 - 746
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 747 through 781 )	A	747 - 781
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 501 through 517 )	B	501 - 517
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 518 through 539 )	B	518 - 539
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 540 through 575 )	B	540 - 575
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 576 through 598 )	B	576 - 598
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 599 through 642 )	B	599 - 642
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 643 through 661 )	B	643 - 661
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 662 through 714 )	B	662 - 714
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 715 through 746 )	B	715 - 746
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 747 through 781 )	B	747 - 781

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