PDB-5hgw: Crystal structure of a peptide deformylase from Burkholderia ambifaria

ID or keywords:

Entry

Database: PDB / ID: 5hgw

Title

Crystal structure of a peptide deformylase from Burkholderia ambifaria

Components

Peptide deformylase

Keywords

HYDROLASE / SSGCID / Peptide deformylase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

peptide deformylase / peptide deformylase activity / co-translational protein modification / translation / metal ion binding
Similarity search - Function

Biological species

Burkholderia ambifaria (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of a peptide deformylase from Burkholderia ambifaria
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Jan 9, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 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_oper_list / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hgw.cif.gz	173.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5hgw.ent.gz	136.4 KB	Display	PDB format
PDBx/mmJSON format	5hgw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hg/5hgw ftp://data.pdbj.org/pub/pdb/validation_reports/hg/5hgw	HTTPS FTP

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Related structure data

Related structure data	4nt8S S: Starting model for refinement
Similar structure data	5cwx-1 5cx0-1 5kob-1 1szz-1 6qxp-3 2mej-d 6qxp-1 1vez-1 1vev-2 5e5d-1 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: SSGCID-BuamA.00078.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Peptide deformylase

B: Peptide deformylase

hetero molecules

42.9 kDa, 2 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)	116.690, 121.350, 71.290
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-315- HOH
2	1	B-327- HOH
3	1	B-569- HOH

#1: Protein	Peptide deformylase / PDF / Polypeptide deformylase Mass: 20902.857 Da / Num. of mol.: 2 / Fragment: BuamA.00078.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia ambifaria (strain MC40-6) (bacteria) Strain: MC40-6 / Gene: def, BamMC406_1925 / Plasmid: BuamA.00078.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1YSH1, peptide deformylase
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 579 / 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: 3.02 Å³/Da / Density % sol: 59.25 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Rigaku ReagentsJCSG+ screen E2: 200mM ammonium sulphate, 200mM NaCl, 100mM Na-cacodylate/HCl pH 6.5; BuamA.00078.a.B1.PS02512 at 17.5 mg/ml, tray 267395 e2, puck pud2-3

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 14, 2015

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. all: 66910 / Num. obs: 66817 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / B_iso Wilson estimate: 12.33 Å² / R_merge F obs: 1 / R_merge(I) obs: 0.054 / R_rim(I) all: 0.056 / Χ²: 0.951 / Net I/σ(I): 29.53 / Num. measured all: 739114

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.6-1.64	7.75	0.898	0.548	4.02	37514	4885	4842	0.587	99.1
1.64-1.69		0.93	0.48	4.55	38425	4776	4753	0.513	99.5
1.69-1.74		0.952	0.415	5.36	38835	4642	4635	0.442	99.8
1.74-1.79		0.969	0.342	6.53	39606	4527	4525	0.363	100
1.79-1.85		0.98	0.277	8.03	39811	4376	4375	0.294	100
1.85-1.91		0.989	0.223	10	40137	4243	4243	0.236	100
1.91-1.98		0.993	0.169	13.3	40195	4098	4098	0.178	100
1.98-2.07		0.996	0.125	18.23	40113	3934	3933	0.131	100
2.07-2.16		0.998	0.101	22.67	39992	3809	3807	0.107	99.9
2.16-2.26		0.999	0.085	27.01	38502	3602	3599	0.089	99.9
2.26-2.39		0.999	0.074	30.87	38288	3458	3457	0.078	100
2.39-2.53		0.999	0.067	34.05	37432	3271	3269	0.07	99.9
2.53-2.7		0.999	0.057	38.59	36664	3088	3088	0.06	100
2.7-2.92		1	0.047	45.15	36171	2879	2878	0.049	100
2.92-3.2		1	0.036	59.11	35925	2653	2653	0.038	100
3.2-3.58		1	0.028	79.26	36926	2415	2415	0.029	100
3.58-4.13		1	0.024	101.76	38456	2141	2140	0.025	100
4.13-5.06		1	0.022	117.92	39435	1836	1835	0.022	99.9
5.06-7.16		1	0.025	100.52	30650	1437	1437	0.026	100
7.16-50		1	0.022	115.19	16037	840	835	0.022	99.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	dev_2276	refinement
PHASER		phasing
PDB_EXTRACT		data extraction
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4nt8

4nt8

Resolution: 1.6→50 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1784	2107	3.15 %	Random selection
R_work	0.1536	64697	-	-
obs	0.1544	66804	99.84 %	-

Solvent computation

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

Displacement parameters

B_iso max: 69.84 Å² / B_iso mean: 17.5828 Å² / B_iso min: 3.72 Å²

Refinement step

Cycle: final / Resolution: 1.6→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2738	0	58	586	3382
B_iso mean	-	-	31.78	29.42	-
Num. residues	-	-	-	-	348

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	3019
X-RAY DIFFRACTION	f_angle_d	1.18	4116
X-RAY DIFFRACTION	f_chiral_restr	0.08	428
X-RAY DIFFRACTION	f_plane_restr	0.008	538
X-RAY DIFFRACTION	f_dihedral_angle_d	14.438	1846

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 (%)
1.6-1.6372	0.2464	144	0.2104	4190	X-RAY DIFFRACTION	99
1.6372-1.6782	0.247	157	0.194	4251	X-RAY DIFFRACTION	99
1.6782-1.7235	0.2307	122	0.1789	4295	X-RAY DIFFRACTION	100
1.7235-1.7743	0.1816	117	0.1675	4291	X-RAY DIFFRACTION	100
1.7743-1.8315	0.2	147	0.1586	4272	X-RAY DIFFRACTION	100
1.8315-1.897	0.1988	143	0.1571	4265	X-RAY DIFFRACTION	100
1.897-1.9729	0.1815	128	0.1615	4325	X-RAY DIFFRACTION	100
1.9729-2.0627	0.1776	128	0.1437	4295	X-RAY DIFFRACTION	100
2.0627-2.1715	0.1604	126	0.141	4335	X-RAY DIFFRACTION	100
2.1715-2.3075	0.1928	136	0.1439	4294	X-RAY DIFFRACTION	100
2.3075-2.4857	0.187	161	0.1458	4297	X-RAY DIFFRACTION	100
2.4857-2.7358	0.1636	157	0.161	4315	X-RAY DIFFRACTION	100
2.7358-3.1316	0.1889	145	0.1616	4356	X-RAY DIFFRACTION	100
3.1316-3.9452	0.1515	131	0.1419	4395	X-RAY DIFFRACTION	100
3.9452-50	0.1569	165	0.1424	4521	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	4.7975	-3.4166	-1.0347	3.2306	0.9069	1.5541	0.0282	0.0925	0.2131	-0.1993	-0.0867	-0.607	0.1399	0.0666	-0.0008	0.1375	0.0311	0.067	0.1121	0.0172	0.2143	28.5977	46.3039	7.3144
2	1.6288	-1.0923	-0.1183	2.2493	0.8565	0.5027	0.1713	0.2474	-0.1189	-0.1963	-0.0763	0.1252	0.0866	0.101	-0.0487	0.1786	0.0565	-0.0278	0.1292	-0.0223	0.0755	15.9536	39.0029	2.3973
3	2.4898	0.564	1.0917	4.2584	2.7725	4.1833	0.1989	0.0884	-0.0531	-0.1837	-0.0518	-0.2117	0.021	0.0447	-0.168	0.0992	0.0459	-0.0037	0.0852	-0.0029	0.1026	27.7272	34.7565	9.1369
4	1.3903	-0.0866	0.1567	1.1511	0.3068	1.2682	0.0737	-0.0192	0.0117	0.07	0.0074	-0.0448	0.0907	0.1633	-0.0865	0.1123	0.029	-0.0006	0.1017	-0.0086	0.0927	21.5324	38.8743	14.2845
5	0.7012	0.1896	-0.4045	3.1293	0.7074	2.6207	0.0788	0.116	-0.0023	-0.0848	-0.0615	-0.0943	0.0673	0.1822	-0.0193	0.1052	0.0435	-0.021	0.122	-0.0031	0.0956	21.9834	39.7287	27.6175
6	3.3281	-2.0759	-2.7854	2.2067	1.0717	2.9155	0.0235	0.2563	-0.2063	0.0205	-0.0951	0.1258	0.0318	-0.1393	0.058	0.0957	-0.0029	-0.0172	0.0647	-0.0155	0.0879	10.4548	32.7061	13.567
7	4.4239	2.2858	0.0446	2.2419	0.0654	0.759	0.1443	-0.209	-0.0036	0.0023	-0.1277	0.0048	0.0352	-0.0211	-0.0132	0.0708	0.0106	-0.0037	0.0651	0.0006	0.0688	11.9189	47.0986	23.5875
8	4.0023	-2.2452	-2.9969	2.5582	2.8669	3.7025	-0.0112	0.153	-0.5224	0.1174	-0.2456	0.1856	0.0587	-0.108	0.2647	0.1193	0.0252	-0.0235	0.0725	-0.0156	0.1468	11.4244	28.4871	14.6475
9	1.2511	0.2878	-0.316	1.8486	1.1281	2.1166	0.0788	0.0124	-0.1929	0.0862	-0.0622	-0.1253	0.1343	0.0792	-0.0028	0.0616	0.0164	-0.013	0.0655	-0.0071	0.1161	11.8925	36.2896	18.2266
10	1.4933	-0.3715	-0.4449	1.032	0.7857	3.9496	0.0545	0.0559	0.1714	-0.1402	-0.195	0.2268	-0.279	-0.2581	0.0616	0.1277	0.008	0.0159	0.0784	-0.004	0.1388	10.2435	53.5043	19.9355
11	4.2555	-2.2836	-1.3449	6.8346	-0.0488	2.8835	0.2502	-0.2656	-0.2181	0.2226	-0.0358	-0.5023	0.2795	0.3732	0.0079	0.1092	-0.0148	-0.0253	0.1164	0.009	0.1567	23.0096	55.7107	28.1705
12	5.4553	4.2897	0.4757	4.1313	0.2181	0.7534	0.1134	-0.0377	-0.1886	0.1945	-0.3112	-0.8679	-0.1517	0.0643	-0.1381	0.1144	-0.0437	-0.0639	0.0995	0.0592	0.2713	28.5457	70.7721	28.919
13	1.11	0.6222	-0.3435	1.784	-0.1567	0.7113	0.0971	-0.022	0.021	0.1279	-0.1182	-0.0986	-0.1096	0.0905	0.0258	0.0921	-0.0281	-0.0195	0.0959	0.017	0.0721	22.4079	81.1348	30.3277
14	1.7999	-0.3721	0.3247	2.4418	0.1131	0.8072	-0.0082	0.3411	0.0343	-0.2548	-0.0175	-0.0793	-0.0766	0.1566	-0.0477	0.1023	-0.034	0.0045	0.1326	0.0111	0.0868	21.3668	78.0383	22.0596
15	4.5715	-0.8907	-2.2694	8.91	-1.3663	1.7104	-0.0807	0.5088	-0.1693	-0.9671	-0.3271	-0.7203	0.4634	-0.1267	-0.1324	0.3857	-0.0799	0.0251	0.4279	0.0313	0.2162	22.2452	76.9643	8.419
16	3.0838	1.7042	2.7574	2.3344	1.3713	2.4543	-0.0491	-0.1312	0.2701	-0.0632	-0.1142	0.1611	-0.0552	-0.105	0.1543	0.078	-0.0012	-0.0116	0.0732	0.0028	0.0815	10.4518	84.2634	22.2926
17	3.9348	-1.847	0.568	1.7309	-0.4399	0.992	0.1676	0.2779	-0.0097	-0.0918	-0.1478	0.0055	0.0538	0.0992	0.0616	0.0899	0.0132	-0.0032	0.088	-0.008	0.0808	12.0258	69.7792	12.5387
18	4.1016	2.4892	2.9416	2.1526	2.3435	2.8025	-0.0631	-0.0297	0.3668	-0.1399	-0.1471	0.261	-0.1338	-0.036	0.3342	0.114	-0.0097	-0.0199	0.075	0.0113	0.1239	11.1692	88.2606	20.5229
19	1.1481	0.0064	0.3556	2.2249	1.0856	1.5907	0.0198	0.0482	0.0919	-0.0826	-0.0845	0.0314	-0.0636	0.0465	-0.0232	0.0501	0.0027	-0.0116	0.0747	0.0023	0.0901	11.3865	76.0179	17.9899
20	6.8678	2.1739	-1.516	3.3373	-0.9491	1.4634	0.0226	0.3165	-0.0935	-0.2836	-0.0564	-0.3646	-0.0328	0.2014	0.153	0.1687	0.0303	0.0132	0.1201	0.0093	0.1173	19.5343	60.6726	8.4428

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 10 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 11 through 25 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 26 through 41 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 42 through 66 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 67 through 76 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 77 through 87 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 88 through 112 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 113 through 125 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 126 through 147 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 148 through 160 )	A
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 161 through 171 )	A
12	X-RAY DIFFRACTION	12	chain 'B' and (resid -2 through 10 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 11 through 41 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 42 through 66 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 67 through 76 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 77 through 87 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 88 through 112 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 113 through 125 )	B
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 126 through 157 )	B
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 158 through 171 )	B

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