PDB-4gxw: Crystal structure of a cog1816 amidohydrolase (target EFI-505188)...

ID or keywords:

Entry

Database: PDB / ID: 4gxw

Title

Crystal structure of a cog1816 amidohydrolase (target EFI-505188) from Burkhoderia ambifaria, with bound Zn

Components

Adenosine deaminase

Keywords

HYDROLASE /

amidohydrolase / cog1816 / adenosine deaminase related protein /

enzyme function initiative / EFI /

Structural Genomics

Function / homology

Function and homology information

adenosine deaminase /

adenosine deaminase activity /

metal ion binding
Similarity search - Function

Biological species

Burkholderia ambifaria (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

Vetting, M.W. / Goble, A.M. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Raushel, F.M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)

Citation

Journal: To be Published
Title: Crystal structure of a cog1816 amidohydrolase (target EFI-505188) from Burkhoderia ambifaria, with bound Zn
Authors: Vetting, M.W. / Goble, A.M. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Raushel, F.M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)

History

Deposition	Sep 4, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 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	4gxw.cif.gz	323 KB	Display	PDBx/mmCIF format
PDB format	pdb4gxw.ent.gz	260.6 KB	Display	PDB format
PDBx/mmJSON format	4gxw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gx/4gxw ftp://data.pdbj.org/pub/pdb/validation_reports/gx/4gxw	HTTPS FTP

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Related structure data

Related structure data	3paoS S: Starting model for refinement
Similar structure data	6ft0-4 6akr-3 2aet-2 3wyl-1 5tkb-1 3tgg-d 6t0e-2 1zkl-d 3sl5-4 6ftw-4 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
Other databases	TargetTrack: EFI-505188

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #158 - Feb 2013 Proton-Gated Urea Channel similarity (1)

Deposited unit

A: Adenosine deaminase

B: Adenosine deaminase

hetero molecules

85.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Adenosine deaminase

hetero molecules

defined by author&software
42.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Adenosine deaminase

hetero molecules

defined by author&software
42.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.058, 66.223, 75.432
Angle α, β, γ (deg.)	90.000, 93.640, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Adenosine deaminase / Mass: 42698.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: AMMD / Gene: Bamb_4621 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B6Q2, adenosine deaminase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1309 / 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: 2.13 Å³/Da / Density % sol: 42.32 %
Crystal grow	Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 6.5 Details: Protein (20 mM Hepes pH 7.5; Reservoir (0.2 M magnesium chloride, 0.1 M MES pH 6.5, 10% Peg4000); Cryoprotection (Reservoir, + 20% Diethylene glycol), sitting drop vapor diffusion, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 13, 2012 / Details: MIRRORS

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.3→75.28 Å / Num. all: 175186 / Num. obs: 175186 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_merge(I) obs: 0.073 / R_sym value: 0.073 / Net I/σ(I): 10.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.3-1.37	2.9	0.567	1.3	72987	25188	0.567	98.3
1.37-1.45	3.5	0.426	1.8	83478	24179	0.426	99.7
1.45-1.55	3.5	0.272	2.7	80242	22717	0.272	99.8
1.55-1.68	3.6	0.178	4.2	76502	21241	0.178	99.9
1.68-1.84	3.7	0.119	6.3	71758	19594	0.119	99.9
1.84-2.06	3.7	0.08	9.3	65330	17682	0.08	99.9
2.06-2.37	3.7	0.058	12.3	57934	15590	0.058	99.8
2.37-2.91	3.7	0.043	15.3	48712	13212	0.043	99.6
2.91-4.11	3.6	0.034	17.5	37009	10184	0.034	99
4.11-75.28	3.6	0.029	18.3	20082	5599	0.029	97.6

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction
MOSFLM		data reduction
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3PAO

3pao

Resolution: 1.3→29.257 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8988 / SU ML: 0.11 / σ(F): 0 / σ(I): 0 / Phase error: 17.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1814	8755	5 %	RANDOM
R_work	0.1601	-	-	-
all	0.1612	175099	-	-
obs	0.1612	175099	99.41 %	-

Solvent computation

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

Displacement parameters

B_iso max: 81.17 Å² / B_iso mean: 16.8155 Å² / B_iso min: 6.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→29.257 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5794	0	4	1309	7107

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6106
X-RAY DIFFRACTION	f_angle_d	1.081	8354
X-RAY DIFFRACTION	f_chiral_restr	0.075	885
X-RAY DIFFRACTION	f_plane_restr	0.006	1116
X-RAY DIFFRACTION	f_dihedral_angle_d	12.09	2209

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.3-1.3148	0.2934	258	0.2637	5327	5585	95
1.3148-1.3302	0.2613	286	0.2515	5411	5697	98
1.3302-1.3465	0.2554	311	0.2374	5543	5854	99
1.3465-1.3635	0.2317	306	0.2222	5487	5793	100
1.3635-1.3814	0.2326	301	0.2108	5524	5825	100
1.3814-1.4004	0.2232	276	0.2051	5527	5803	100
1.4004-1.4204	0.2329	252	0.2001	5568	5820	100
1.4204-1.4416	0.2026	297	0.1905	5597	5894	100
1.4416-1.4641	0.2138	270	0.1829	5522	5792	100
1.4641-1.4881	0.192	295	0.175	5534	5829	100
1.4881-1.5138	0.1929	341	0.1698	5540	5881	100
1.5138-1.5413	0.1785	295	0.1631	5580	5875	100
1.5413-1.5709	0.1993	299	0.1562	5504	5803	100
1.5709-1.603	0.1641	281	0.1494	5544	5825	100
1.603-1.6378	0.1902	305	0.1497	5532	5837	100
1.6378-1.6759	0.1791	281	0.1466	5590	5871	100
1.6759-1.7179	0.1687	280	0.1474	5573	5853	100
1.7179-1.7643	0.1632	313	0.1471	5530	5843	100
1.7643-1.8162	0.1801	279	0.1491	5588	5867	100
1.8162-1.8748	0.1617	302	0.1526	5559	5861	100
1.8748-1.9418	0.2096	298	0.1656	5567	5865	100
1.9418-2.0195	0.1824	302	0.1467	5577	5879	100
2.0195-2.1114	0.1621	291	0.1436	5545	5836	100
2.1114-2.2227	0.1676	278	0.1453	5618	5896	100
2.2227-2.3619	0.1793	291	0.1574	5581	5872	100
2.3619-2.5442	0.1727	287	0.1486	5575	5862	100
2.5442-2.8	0.1755	286	0.1488	5592	5878	100
2.8-3.2048	0.165	280	0.1547	5566	5846	99
3.2048-4.036	0.156	324	0.1439	5546	5870	99
4.036-29.2649	0.171	290	0.1529	5597	5887	97

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	0.7542	0.4457	-0.3012	0.864	-0.0012	0.2606	-0.0111	0.0128	0.186	-0.0047	0.029	0.2527	-0.0425	-0.0889	-0.0123	0.109	0.0036	-0.0048	0.119	0.0006	0.1764	-50.1011	-26.1504	17.9899
2	0.8402	0.334	0.0681	0.7527	0.364	1.5594	0.0466	-0.0568	0.6487	-0.3019	-0.2883	0.3312	-0.5107	-0.0274	0.142	0.2771	0.0456	-0.0109	0.2171	-0.1435	0.4488	-35.7999	-11.0303	27.6873
3	0.7946	0.3536	0.2102	0.4689	0.1515	0.3365	0.0139	-0.0958	0.0257	0.0461	-0.0267	0.0269	-0.0225	-0.0262	0.0109	0.1037	-0.0111	0.0023	0.1204	-0.0063	0.0817	-29.7828	-27.0527	28.1531
4	0.7261	-0.2047	-0.1364	0.2927	0.2281	0.9018	0.0053	-0.0328	0.0075	0.0078	0.0036	-0.0374	0.0219	0.1069	-0.0057	0.084	-0.0032	-0.0041	0.0929	-0.0006	0.0888	-22.4015	-30.8361	14.0631
5	0.9205	-0.0097	-0.1723	0.9113	-0.1128	0.5753	-0.0179	0.1186	0.0139	-0.0889	0.0111	0.0697	0.0145	-0.0227	0.0071	0.0971	-0.0082	-0.0054	0.0988	0.0013	0.0899	-34.7791	-28.8325	1.884
6	1.0265	0.2935	-0.2641	0.9316	-0.1488	0.4443	-0.0194	0.0274	0.0457	-0.0232	0.0141	0.0984	0.0129	-0.0723	0.0044	0.0879	-0.0062	-0.0151	0.0933	-0.0023	0.1128	-48.7817	-32.6183	12.6582
7	0.2472	0.2539	-0.0852	0.5301	-0.15	0.4098	-0.0004	-0.0305	0.0389	0.0058	0.0483	0.1434	-0.0305	-0.1725	-0.0466	0.0971	0.0076	0.005	0.1382	0.0096	0.1183	-13.225	8.1782	18.0184
8	0.8801	-0.4193	0.6279	0.7851	-0.5672	0.935	-0.0375	-0.1066	0.2631	0.07	-0.0308	-0.1553	-0.2127	-0.0121	0.0481	0.1649	0.0117	0.0041	0.1469	-0.0362	0.1584	3.7728	21.6866	33.0425
9	0.6694	0.0165	-0.0417	0.3761	0.0958	0.6124	0.007	-0.0873	-0.0168	0.0272	-0.0086	-0.0085	0.004	0.0022	0.0049	0.0818	-0.0029	-0.005	0.0843	0.0042	0.0685	7.8082	5.8879	24.7637
10	0.8772	-0.047	-0.2373	0.3158	0.0343	0.9692	-0.0052	-0.0297	-0.0655	0.0035	0.0002	-0.0034	0.02	0.0833	0.0006	0.0831	0.003	0.006	0.0761	0.0009	0.0808	13.5255	1.4461	11.2141
11	0.7793	-0.2251	-0.2495	0.7621	0.215	0.4601	0.0086	0.1208	-0.0193	-0.1065	-0.0364	0.0228	-0.0144	-0.0433	0.0252	0.1135	0.0033	-0.0035	0.0989	-0.0006	0.085	1.8262	5.0224	2.1571
12	0.3245	-0.5898	-0.3199	2.6011	1.1125	0.497	0.1024	0.1659	0.0495	-0.2639	-0.0689	0.1541	-0.1384	-0.1268	-0.0284	0.1436	0.0263	-0.0086	0.1323	0.0153	0.1196	-10.5963	13.6281	2.5384
13	0.6428	0.1277	0.0598	0.3304	-0.176	0.6199	0.0095	-0.0082	-0.0063	-0.0262	0.0062	0.0311	0.0553	-0.0996	-0.0163	0.0929	-0.0049	-0.0063	0.0949	0.0078	0.0925	-9.8432	2.6923	13.1162
14	1.6064	-0.3376	-0.0486	1.3911	-0.095	1.0988	-0.0203	0.0267	-0.0527	-0.0856	0.0265	0.1074	0.2102	-0.2411	0.0095	0.1675	-0.0655	-0.0067	0.1605	0.0198	0.1729	-15.3423	-10.2554	17.0909

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 42 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 75 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 76 through 147 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 148 through 216 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 217 through 273 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 274 through 371 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 3 through 42 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 43 through 65 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 66 through 176 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 177 through 216 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 217 through 273 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 274 through 291 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 292 through 341 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 342 through 366 )	B

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