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- PDB-9qft: Crystal structure of Def2 in complex with actinonin -

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Basic information

Entry
Database: PDB / ID: 9qft
TitleCrystal structure of Def2 in complex with actinonin
ComponentsPeptide deformylase 2
KeywordsHYDROLASE / metalloprotease / antibiotic / protein translation
Function / homology
Function and homology information


peptide deformylase / : / peptide deformylase activity / translation / metal ion binding
Similarity search - Function
Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase
Similarity search - Domain/homology
ACTINONIN / NICKEL (II) ION / Peptide deformylase 2
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLamberioux, M. / Mechaly, A. / Haouz, A. / Mazel, D.
Funding support France, 1items
OrganizationGrant numberCountry
Pasteur Institute France
CitationJournal: 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
DepositionMar 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Peptide deformylase 2
D: Peptide deformylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7986
Polymers39,9092
Non-polymers8884
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.890, 72.890, 150.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "D" and (resid 15 through 118 or resid 120 through 174))
d_2ens_1(chain "G" and (resid 15 through 118 or resid 120 through 174))
d_1ens_2chain "E"
d_2ens_2chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALSERSERDB15 - 11815 - 118
d_12ens_1VALVALHISHISDB120 - 174120 - 174
d_21ens_1VALVALSERSERGA15 - 11815 - 118
d_22ens_1VALVALHISHISGA120 - 174120 - 174
d_11ens_2BB2BB2BB2BB2DE1001
d_21ens_2BB2BB2BB2BB2GC1001

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.856301922963, -0.415776895181, 0.306392868984), (-0.442778276527, -0.896383491573, 0.0210721112396), (0.265884212707, -0.153708195844, -0.951671884613)-20.4905392407, 26.5820379872, 3.39109710106
2given(0.850612450317, -0.476194858298, 0.222928051839), (-0.483023622576, -0.875206833291, -0.0264797846268), (0.20771769159, -0.0851554806879, -0.974475194507)-18.7633420777, 26.9823124367, 2.5374518343

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Components

#1: Protein Peptide deformylase 2 / PDF 2 / Polypeptide deformylase 2


Mass: 19954.689 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: def2, VC_A0150 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KN16, peptide deformylase
#2: 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
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% (w/v) PEG4K, 10% (v/v) 2-Propanol, 0,1M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.82→48.77 Å / Num. obs: 37514 / % possible obs: 99.94 % / Redundancy: 26 % / Biso Wilson estimate: 37.97 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05959 / Rpim(I) all: 0.01198 / Rrim(I) all: 0.06082 / Net I/σ(I): 28.72
Reflection shellResolution: 1.82→1.86 Å / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2780 / CC1/2: 0.912 / CC star: 0.977 / Rpim(I) all: 0.2791 / Rrim(I) all: 1.389

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→48.77 Å / SU ML: 0.2418 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.6764
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2197 1875 5 %
Rwork0.1805 35616 -
obs0.1823 37491 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.1 Å2
Refinement stepCycle: LAST / Resolution: 1.82→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 56 213 2819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722643
X-RAY DIFFRACTIONf_angle_d1.00553585
X-RAY DIFFRACTIONf_chiral_restr0.0641429
X-RAY DIFFRACTIONf_plane_restr0.0063464
X-RAY DIFFRACTIONf_dihedral_angle_d18.58111059
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BDX-RAY DIFFRACTIONTorsion NCS0.815050686279
ens_2d_2EDX-RAY DIFFRACTIONTorsion NCS0.528213789762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.38021380.38142636X-RAY DIFFRACTION98.19
1.86-1.920.33991420.2922698X-RAY DIFFRACTION99.82
1.92-1.980.261420.22382686X-RAY DIFFRACTION100
1.98-2.050.25811410.21272676X-RAY DIFFRACTION99.75
2.05-2.130.23761420.21442705X-RAY DIFFRACTION99.96
2.13-2.230.24471430.20872717X-RAY DIFFRACTION99.97
2.23-2.350.21951440.19642724X-RAY DIFFRACTION100
2.35-2.50.27251420.20832714X-RAY DIFFRACTION100
2.5-2.690.25071440.2052737X-RAY DIFFRACTION100
2.69-2.960.25261450.21772754X-RAY DIFFRACTION100
2.96-3.390.22581460.18842772X-RAY DIFFRACTION99.97
3.39-4.270.18261490.15062821X-RAY DIFFRACTION99.97
4.27-48.770.18931570.14562976X-RAY DIFFRACTION99.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
14.998744326211.777838712952.861818981375.665008290163.831587897736.298102149260.395632374343-0.0200677646305-0.6807305355560.6722650294530.0283266649468-0.3761622307511.150508104690.269881165133-0.3595896897810.5015681457340.121363122877-0.0531828903990.2504161972810.02724504110490.390881833692-14.3489958973.39477018003-15.8546192509
20.503771692895-0.6337150981650.619917645991.61833571774-0.8653852186044.317598651120.07375462793170.104679193969-0.233604024229-0.130414026296-0.04077778064640.0003455106798030.8247900007880.3660026112380.01524002725170.3968346477380.0494075075773-0.03004395451580.249202906214-0.01538685738420.292145206277-17.819520151110.4041933155-24.0016601689
33.49701314129-0.951644672980.8202346112174.632129490220.5465872809023.00123114460.102538309765-0.149163638872-0.1835158686110.1572514936490.04755495463420.1753110191820.881185883794-0.266654391849-0.07026062669350.442993584266-0.015919920025-0.03304270724970.2490256692980.02588267489870.335680995425-21.94034343459.00945590071-14.2008378199
40.9971215398550.1663112254511.90555324885.09589283791-0.4994206663313.801700646370.1686460140560.0269833336229-0.288746207421-0.463488342163-0.187178853707-0.4572058700050.2305123576310.501372480627-0.03343369781530.3014864659420.0306872220428-0.01741748983910.191889901657-0.007367307521160.24500577429-17.074231015212.4620640293-22.9286253935
53.070885576311.510056082741.017306666595.12885667789-0.01259891474011.29743207487-0.00185151584014-0.591003604099-0.4236430924490.4059012285110.3550849121171.880323698720.605834272355-1.55458696774-0.09962559495090.415483344913-0.2036034341550.04314404727090.5871748766210.05875683879980.649635571883-34.860181590411.9062656738-16.4107012279
60.849186830286-0.8937290565670.4488982741852.634206707031.167875588072.06393856395-0.1048454300250.02436752092240.161643356551-0.05794908189550.0962326611145-0.167046033021-0.37444015343-0.000242360766308-0.009491222788390.3054007051898.71425263559E-5-0.0292552557240.200445552846-0.002736338990590.249535992643-21.325164947224.4959902033-21.5747310182
71.61114569293-0.5841067903250.6262642930722.432736057090.01385513939392.06767154156-0.115662697267-0.120011058995-0.03376450655310.309547403280.07651839760220.111178564864-0.0978436936662-0.2583673988120.0001128358245680.2924658415220.0139182979353-0.01198763416410.211414999670.0004366947381570.244330152075-21.805238298321.1512036432-11.6199808479
82.3803104165-0.870945333745-1.660278605722.130471124340.554431830375.55152664281-0.04405609208180.1604887433130.159119107303-0.112986095971-0.2058829206650.287162112453-0.395846213622-0.9420849176480.05982845169070.317233905040.0298093712454-0.04709070009410.275873718074-0.009822498763430.327639902832-28.535055264627.6776616305-20.8660729309
90.206013845898-0.4178244299910.4187152540940.583244850736-0.8535103196071.69677726887-0.217713766732-0.1691220329890.1302910967490.3056984040750.0452608039616-0.16960167495-0.08266439978510.009381889593660.1777990929950.404730213060.00533717894957-0.04934800127380.2470848686950.01795969710050.27574878912-17.201801109919.8188527167-10.8425053936
101.542761356280.931748297608-0.6279939656764.032340771821.524635145111.97037674376-0.208295427558-0.0556161400821-0.265033998948-0.3425346958020.1754427842410.1614722954830.359604005539-0.09010962844390.09539719640670.501324102193-0.00542323029179-0.1027050331480.3677438596630.09452137378360.440706078046-12.63081319225.58629022887-0.0403407093164
110.2912198263-0.06587344337130.6669172928332.31559049623-0.04968028213773.503633613380.0779058592282-0.7452219169570.6626606672511.68723896765-0.558574380851-1.38804193916-1.445977796471.21698953352-0.06355038144781.37034841862-0.334313280704-0.4446548638240.444125820641-0.07290623336310.894687449634.3237120514117.872243843124.7691608219
122.378036831420.154798006647-0.9086002308473.12407948684-1.08333280352.584648564040.115076844246-0.3258784400470.4549678620641.30166250516-0.12597120905-0.485654930467-0.999115479205-0.0003952953726450.04555578033420.851363778121-0.0652129364216-0.1746250522240.328107816184-0.003825526083190.463740637219-3.5148385458215.130408045719.3582281181
132.573060635931.12678570145-0.3174102204226.37836276729-2.465971899453.33623810143-0.0311281352089-0.004623677756370.2360561434280.545010343488-0.105034767885-0.292698845713-0.442696352789-0.1377508578180.0754132161890.395380122523-0.00927546783613-0.06328705084630.2999322370780.0105410676990.392306980205-4.556415707697.7447821704415.2265521913
141.623607481430.549369206439-0.4026764689131.90166896276-0.5829514179322.03861052832-0.115848150139-0.139378512948-0.1639573763550.747818927635-0.321771113347-0.831915330759-0.2898440542930.5566050114630.3794160555850.436091834877-0.0570025215485-0.142526329720.3400338199360.1344745118030.5664001622532.001831724486.9320928892914.4584459933
150.4886435169920.335980920076-1.131144710820.341735353809-1.030992257613.372131024640.0668523233632-0.8053627389471.833835439091.05936126997-0.297672968636-0.874863340924-2.190038421481.228288747230.4052504169610.810260086994-0.156485482769-0.2537787162220.959766536195-0.003405984346611.4192414143615.007053912211.52383738344.16922082217
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'G' and (resid 13 through 23 )GA13 - 231 - 11
22chain 'G' and (resid 24 through 52 )GA24 - 5212 - 40
33chain 'G' and (resid 53 through 64 )GA53 - 6441 - 52
44chain 'G' and (resid 65 through 73 )GA65 - 7353 - 61
55chain 'G' and (resid 74 through 82 )GA74 - 8262 - 70
66chain 'G' and (resid 83 through 94 )GA83 - 9471 - 82
77chain 'G' and (resid 95 through 129 )GA95 - 12983 - 117
88chain 'G' and (resid 130 through 137 )GA130 - 137118 - 125
99chain 'G' and (resid 138 through 160 )GA138 - 160126 - 148
1010chain 'G' and (resid 161 through 180 )GA161 - 180149 - 168
1111chain 'D' and (resid 15 through 51 )DD15 - 511 - 37
1212chain 'D' and (resid 52 through 95 )DD52 - 9538 - 81
1313chain 'D' and (resid 96 through 137 )DD96 - 13782 - 123
1414chain 'D' and (resid 138 through 160 )DD138 - 160124 - 146
1515chain 'D' and (resid 161 through 174 )DD161 - 174147 - 160

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