PDB-9qfr: Crystal structure of Def1 in complex with actinonin

ID or keywords:

Entry

Database: PDB / ID: 9qfr

Title

Crystal structure of Def1 in complex with actinonin

Components

Peptide deformylase 1

Keywords

HYDROLASE / metalloprotease / antibiotic / protein translation

Function / homology

Function and homology information

peptide deformylase / : / peptide deformylase activity / translation / metal ion binding
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.52 Å

Authors

Mechaly, A. / Lamberioux, M. / Haouz, A. / Mazel, D.

Funding support

1items

Citation

Journal: Mol.Biol.Evol. / Year: 2025
Title: Unraveling the Prevalence and Multifaceted Roles of Accessory Peptide Deformylases in Bacterial Adaptation and Resistance.
Authors: Lamberioux, M. / Ducos-Galand, M. / Kaminski, P.A. / Littner, E. / Betton, J.M. / Mechaly, A. / Haouz, A. / Mazel, D.

History

Deposition	Mar 12, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 10, 2025	Provider: repository / Type: Initial release
Revision 1.1	Dec 24, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9qfr.cif.gz	195.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9qfr.ent.gz	127.1 KB	Display	PDB format
PDBx/mmJSON format	9qfr.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/qf/9qfr ftp://data.pdbj.org/pub/pdb/validation_reports/qf/9qfr	HTTPS FTP

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Related structure data

Related structure data	9qftC C: citing same article (ref.)
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: Peptide deformylase 1

B: Peptide deformylase 1

hetero molecules

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

1

A: Peptide deformylase 1

hetero molecules

defined by author
Evidence: gel filtration
20.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Peptide deformylase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	41.780, 44.480, 213.660
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 0 through 41 or resid 43 through 167))
d_2	ens_1	(chain "B" and (resid 0 through 41 or resid 43 through 167))
d_1	ens_2	chain "C"
d_2	ens_2	chain "D"

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	ens_1	GLY	GLY	ALA	ALA	A	A	0 - 41	12 - 53
d_1	2	ens_1	GLU	GLU	GLU	GLU	A	A	43 - 167	55 - 179
d_2	1	ens_1	GLY	GLY	ALA	ALA	B	B	0 - 41	12 - 53
d_2	2	ens_1	GLU	GLU	GLU	GLU	B	B	43 - 167	55 - 179
d_1	1	ens_2	NI	NI	NI	NI	A	C	201
d_1	2	ens_2	BB2	BB2	BB2	BB2	A	D	202
d_2	1	ens_2	NI	NI	NI	NI	B	E	201
d_2	2	ens_2	BB2	BB2	BB2	BB2	B	F	202

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.138023983816, 0.989930366401, 0.031420527819), (0.988518344995, -0.139657924698, 0.0576814153524), (0.0614887103425, 0.0230983494195, -0.997840470594)	7.60227581997, -11.9171504184, 52.3907704795
2	given	(0.256469057785, 0.965647019775, 0.0418264939842), (0.964960512816, -0.258289421759, 0.0462361688826), (0.0554511596327, 0.0285027684154, -0.998054488036)	5.02511600776, -12.161209729, 52.3091293889

#1: Protein	Peptide deformylase 1 / PDF 1 / Polypeptide deformylase 1 Mass: 20433.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Gene: def1, VC_0046 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KVU3, peptide deformylase
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-BB2 / ACTINONIN / 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE Mass: 385.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₃₅N₃O₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: antitumor, antibiotic*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.36 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 20% (w/v) PEG4K, 20% (v/v) 2-Propanol and 0,1M Na3-citrate pH 5.6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 16, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.52→41 Å / Num. obs: 62085 / % possible obs: 99.45 % / Redundancy: 14.4 % / B_iso Wilson estimate: 23.73 Å² / CC_1/2: 0.997 / CC star: 0.999 / R_merge(I) obs: 0.1141 / R_pim(I) all: 0.0313 / R_rim(I) all: 0.1184 / Net I/σ(I): 10.99
Reflection shell	Resolution: 1.52→1.55 Å / Redundancy: 13.9 % / R_merge(I) obs: 0.7088 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 2498 / CC_1/2: 0.882 / CC star: 0.968 / R_pim(I) all: 0.1943 / R_rim(I) all: 0.736 / % possible all: 88.9

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
autoPROC		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.52→41 Å / SU ML: 0.1592 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 18.4663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2057	3104	5 %
R_work	0.175	58966	-
obs	0.1764	62070	99.45 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 36.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.52→41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2652	0	56	430	3138

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0064	2747
X-RAY DIFFRACTION	f_angle_d	0.9789	3715
X-RAY DIFFRACTION	f_chiral_restr	0.0584	433
X-RAY DIFFRACTION	f_plane_restr	0.0076	490
X-RAY DIFFRACTION	f_dihedral_angle_d	18.4499	1117

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	1.06560719688
ens_2	d_2	C	A	X-RAY DIFFRACTION	Torsion NCS	0.540534023688

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 (%)
1.52-1.55	0.2531	125	0.2475	2373	X-RAY DIFFRACTION	88.9
1.55-1.57	0.2462	138	0.2381	2622	X-RAY DIFFRACTION	100
1.57-1.6	0.2091	142	0.2021	2682	X-RAY DIFFRACTION	99.93
1.6-1.63	0.2176	137	0.1883	2607	X-RAY DIFFRACTION	100
1.63-1.66	0.1958	141	0.1812	2682	X-RAY DIFFRACTION	100
1.66-1.69	0.2281	140	0.1914	2663	X-RAY DIFFRACTION	100
1.69-1.73	0.2252	140	0.1989	2652	X-RAY DIFFRACTION	99.96
1.73-1.77	0.2491	140	0.2326	2655	X-RAY DIFFRACTION	99.93
1.77-1.81	0.2255	140	0.227	2668	X-RAY DIFFRACTION	99.93
1.81-1.86	0.2398	140	0.2231	2660	X-RAY DIFFRACTION	100
1.86-1.92	0.2476	140	0.2052	2662	X-RAY DIFFRACTION	100
1.92-1.98	0.209	142	0.1932	2685	X-RAY DIFFRACTION	99.93
1.98-2.05	0.2193	140	0.1874	2675	X-RAY DIFFRACTION	99.93
2.05-2.13	0.2094	141	0.1912	2675	X-RAY DIFFRACTION	99.96
2.13-2.23	0.2315	142	0.1878	2700	X-RAY DIFFRACTION	99.96
2.23-2.35	0.2082	143	0.1871	2711	X-RAY DIFFRACTION	100
2.35-2.49	0.2222	141	0.1901	2675	X-RAY DIFFRACTION	99.96
2.49-2.69	0.2318	143	0.189	2712	X-RAY DIFFRACTION	100
2.69-2.96	0.2087	144	0.1835	2740	X-RAY DIFFRACTION	99.9
2.96-3.38	0.2138	145	0.1699	2752	X-RAY DIFFRACTION	100
3.38-4.26	0.1717	146	0.1449	2780	X-RAY DIFFRACTION	100
4.26-41	0.1743	154	0.1407	2935	X-RAY DIFFRACTION	99.55

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	2.58794130919	1.53673208954	0.372818999299	2.00336346656	-1.31869904933	2.45652073546	-0.140143992372	0.55851809694	-0.210198467189	-0.205477761372	-0.0837059561175	0.14360419142	0.0632006254448	-0.654669741519	0.332521794671	0.206500822248	0.0186689919931	-0.015213352517	0.174928769188	-0.0528194499008	0.255818016811	6.47798948436	-2.14642895954	1.80882341492
2	5.47551086296	0.489986279552	-3.30951646693	4.35202313513	-0.127864266027	4.47799138377	0.318960285979	-0.0776217059058	0.322524538054	-0.391273656773	-0.0658703161444	0.0964130993982	-0.715293943157	0.0488967443223	-0.296892206187	0.19361366171	0.0545865071699	-0.0347762058978	0.104373946161	0.0112491333832	0.192311451828	9.70810942229	11.1308918494	6.02860506544
3	3.51017622487	-0.969080947462	0.278412700078	3.09303830338	0.587698939023	4.30474887771	0.0919731862206	-0.0266194062719	-0.24610942774	0.069774270345	-0.174084909123	0.314484644434	0.150371437281	-0.231193020862	0.0734969914416	0.141914909658	-0.0398172316931	0.0181867025495	0.193840843757	-0.0493849060714	0.281725380372	3.35885914881	0.507149679895	14.0539152951
4	2.29265724801	-1.69404936811	0.128612225844	2.40686652224	-1.75417997917	4.27054684143	0.06429098397	0.142147491544	-0.193667297641	-0.165910351333	-0.174860205662	0.250500556368	0.216171437023	-0.0370766496173	0.0754645075174	0.182387961684	-0.0105281346717	0.0087753949954	0.158669693797	-0.0515220412157	0.256740361445	10.5348963776	0.925294454079	8.68896265179
5	4.83091906562	4.57667330642	-3.54368858517	4.61415579282	-3.59990703563	3.09402913567	0.102095726549	-0.286623886743	-0.788121007588	0.588285346267	-0.277007721539	-0.784079947302	0.88532027392	-0.13317082069	0.21961422256	0.435095331607	-0.0249065185258	0.0152747943132	0.21857530315	0.0158124561915	0.314974287133	13.1996476101	-9.39899912262	20.463661167
6	2.44274849842	-3.19693987242	-0.409072022013	4.59401994662	1.31626465523	0.919254855714	0.0522325729563	-0.15845206075	0.759644023817	-0.0669310849268	0.0669458071772	-0.343341716846	-0.028390451895	0.187563898632	-0.0819487494909	0.196049950883	0.00113091178289	0.0272996430472	0.202990643167	-0.028988115434	0.24059943927	20.6678308557	7.80563352026	17.340896906
7	2.63762658835	-0.223502875715	-0.180611874262	1.07753172431	0.720614566469	1.00675715797	-0.0188047846311	-0.102122884479	-0.0377872702663	0.054901060042	0.114631167129	-0.00964066227982	0.0693020303836	0.143990989844	-0.109471701921	0.202390530137	0.000308375003611	0.0111823128073	0.15090117633	-0.00668699709256	0.200705517531	21.4262248276	-0.544218013029	11.814727508
8	1.55701114191	-0.34265835852	-0.807792572076	0.983513647017	1.04532094444	4.17593991989	0.0379092169223	-0.144474064028	0.0364216295531	-0.0404856805739	0.057608164785	-0.0226960987614	-0.0563447221618	0.133251406524	-0.106387930454	0.187979144239	-0.0171237026258	0.019761319811	0.168211506375	-0.0482905510946	0.246276966157	21.7803595586	1.84180972611	10.7816335927
9	5.6491116617	6.75966635325	3.86177577726	8.38473314737	3.37335020167	5.46172505125	-0.421397685333	0.335931147452	0.0755089094369	-0.419509347352	0.331936150061	0.0750284217208	-0.0793081042706	-0.0743247620057	0.054317333126	0.28606038324	-0.0131299606219	0.00762410127334	0.141169205686	0.000918906986985	0.188631960869	15.7156212243	-6.92183020565	-10.6993256116
10	2.99579789121	-0.416603624954	-0.883602826522	1.76124956613	0.536171110409	3.89627105144	-0.20164837329	-0.674053296388	-0.518877756412	0.325526714891	-0.0025261772573	0.211238490944	0.379171182006	-0.0442366199287	0.212328523148	0.289148652325	-0.0499768034642	0.0656615991286	0.473793250231	0.083149491715	0.234981546381	11.377729512	-4.4948360952	44.3995224051
11	5.26034517187	4.87875692964	5.31619348383	4.49972306179	4.9421501957	5.43352753953	-0.0399853634302	0.947819105221	0.480322060855	0.0271586424204	-0.22975318829	0.857310004177	0.0598060910922	-0.806212354711	0.247944860903	0.281776210867	-0.0268926639557	7.13599644454E-5	0.642228173351	-0.0219371216686	0.37964694986	0.930771644958	4.09085102842	32.1300339561
12	3.08420271662	-0.0800909537363	-0.278002462714	2.14579701945	2.33962489752	2.803118404	0.0274379364578	-0.295393065955	0.173939642176	-0.0082960413309	0.112802228445	-0.328398894058	-0.33556092636	0.319843347187	-0.122702566416	0.283397878152	-0.0663970901214	0.0422166160924	0.422623529596	-0.0202568712232	0.235022887388	18.8302736469	8.45679721881	36.8714496131
13	6.0342623934	2.24650694589	-6.06625485978	5.67282699709	-6.01679223159	9.54131167858	0.334675152952	-0.471972904277	0.185031158053	0.417253744844	-0.223370836793	0.409573682643	-0.555820094229	-0.305122532903	-0.225321690435	0.286310473229	-0.0407712693982	-8.67697238049E-5	0.491868527786	-0.087679762655	0.199074698694	4.15941102075	12.0911562188	48.2475763787
14	1.59516350755	-1.70564304798	-2.02146898241	2.22806378211	2.23673546654	5.45198780327	0.105844624465	-0.337434842056	0.0828101691535	-0.0287563373182	0.0819199352388	-0.103128700033	-0.231720025579	0.114611143261	-0.193906164664	0.21743971635	-0.0590084960692	0.0351972661833	0.402559712245	-0.0570486531795	0.228562568721	13.5697530007	9.36480082097	40.8461446725
15	8.13580311185	7.10074492315	-4.89089066836	6.161567014	-4.52335406524	3.16624809068	0.283750274789	-0.421187160808	0.180750357806	0.741981575018	-0.177895160067	0.313666785425	-0.0790182800543	0.201567119391	-0.0340391420256	0.347312994992	-0.0257979795138	0.0450793181343	0.468861565354	0.015094623749	0.206299847329	3.55317999447	4.45321634704	64.4511308785

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 0 through 11 )	A	A	0 - 11	1 - 12
2	2	chain 'A' and (resid 12 through 25 )	A	A	12 - 25	13 - 26
3	3	chain 'A' and (resid 26 through 41 )	A	A	26 - 41	27 - 42
4	4	chain 'A' and (resid 42 through 61 )	A	A	42 - 61	43 - 62
5	5	chain 'A' and (resid 62 through 70 )	A	A	62 - 70	63 - 71
6	6	chain 'A' and (resid 71 through 82 )	A	A	71 - 82	72 - 83
7	7	chain 'A' and (resid 83 through 117 )	A	A	83 - 117	84 - 118
8	8	chain 'A' and (resid 118 through 148 )	A	A	118 - 148	119 - 149
9	9	chain 'A' and (resid 149 through 167 )	A	A	149 - 167	150 - 168
10	10	chain 'B' and (resid 0 through 61 )	B	D	0 - 61	1 - 62
11	11	chain 'B' and (resid 62 through 70 )	B	D	62 - 70	63 - 71
12	12	chain 'B' and (resid 71 through 82 )	B	D	71 - 82	72 - 83
13	13	chain 'B' and (resid 83 through 98 )	B	D	83 - 98	84 - 99
14	14	chain 'B' and (resid 99 through 148 )	B	D	99 - 148	100 - 149
15	15	chain 'B' and (resid 149 through 167 )	B	D	149 - 167	150 - 168

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Yorodumi