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- PDB-6ck7: Crystal structure of a peptide deformylase from Legionella pneumo... -

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Basic information

Entry
Database: PDB / ID: 6ck7
TitleCrystal structure of a peptide deformylase from Legionella pneumophila bound to actinonin
ComponentsPeptide deformylase
KeywordsHYDROLASE/ANTIBIOTIC / National Institute of Allergy and Infectious Diseases / NIAID / structural genomics / Legionnaires' disease / formyl-L-methionyl peptide / formate / methionyl peptide / Seattle Structural Genomics Center for Infectious Disease / SSGCID / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / : / translation / metal ion binding
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACTINONIN / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structures of Legionella pneumophila serogroup 1 peptide deformylase bound to nickel(II) and actinonin.
Authors: Nguyen, C.L. / Fan, W. / Fisher, S. / Matthews, K. / Norman, J.O. / Abendroth, J. / Barrett, K.F. / Craig, J.K. / Edwards, T.E. / Lorimer, D.D. / McLaughlin, K.J.
History
DepositionFeb 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Apr 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide deformylase
B: Peptide deformylase
C: Peptide deformylase
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,43917
Polymers81,1554
Non-polymers2,28413
Water11,422634
1
A: Peptide deformylase
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6718
Polymers40,5772
Non-polymers1,0946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-111 kcal/mol
Surface area15330 Å2
MethodPISA
2
C: Peptide deformylase
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7679
Polymers40,5772
Non-polymers1,1907
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-128 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.650, 132.060, 90.380
Angle α, β, γ (deg.)90.000, 103.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptide deformylase / PDF / Polypeptide deformylase


Mass: 20288.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria)
Gene: def_2, def, def_1, def_3, A1D14_13265, A9P85_13750, ERS240541_01674, ERS240560_02189, ERS253249_00325, lpymg_02824
Production host: Escherichia coli (E. coli)
References: UniProt: A0A128NM93, UniProt: Q5ZSC4*PLUS, peptide deformylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#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.: 4 / Source method: obtained synthetically / Formula: C19H35N3O5 / Comment: antibiotic*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O
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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16.2 mg/mL LepnA.00882.a.B1.PW38390 + 2 mM actinonin against Wiz III/IV screen condition C6 (25.5% PEG4000, 0.17 M ammonium, 15% glycerol), cryoprotection: direct, crystal tracking ID ...Details: 16.2 mg/mL LepnA.00882.a.B1.PW38390 + 2 mM actinonin against Wiz III/IV screen condition C6 (25.5% PEG4000, 0.17 M ammonium, 15% glycerol), cryoprotection: direct, crystal tracking ID 297899c6, unique puck ID iap4-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2018
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.65→43.391 Å / Num. obs: 119433 / % possible obs: 97.9 % / Redundancy: 3.162 % / Biso Wilson estimate: 22.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.044 / Χ2: 1.08 / Net I/σ(I): 15.82 / Num. measured all: 377650 / Scaling rejects: 449
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.692.2070.3112.4818019896681630.8740.39691
1.69-1.742.6110.2933.0122763879087170.8940.36599.2
1.74-1.792.9220.2364.0625005858685570.9350.28999.7
1.79-1.843.3150.1945.4127188820382010.9640.232100
1.84-1.913.3370.1566.8326708803080040.9770.18799.7
1.91-1.973.2250.129.1124735776976700.9830.14498.7
1.97-2.053.430.0911.9125723753774990.9910.10699.5
2.05-2.133.3240.07614.2723739723371420.9930.0998.7
2.13-2.223.4430.06217.0623599692968550.9950.07398.9
2.22-2.333.2270.05718.5520768658864350.9950.06997.7
2.33-2.463.3830.0520.8620990630562040.9960.0698.4
2.46-2.613.2970.04522.919242595558370.9970.05498
2.61-2.793.380.03925.8518572563154940.9970.04697.6
2.79-3.013.2070.03627.7916271521550740.9970.04397.3
3.01-3.33.2690.03130.8815166476346400.9980.03797.4
3.3-3.693.2760.02833.7213815436942170.9980.03396.5
3.69-4.263.2210.02634.6611962384437140.9990.03196.6
4.26-5.223.2770.02435.7910373326831650.9990.02996.8
5.22-7.383.4540.02635.698563253924790.9990.0397.6
7.38-43.3913.2570.02236.444449141413660.9990.02696.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CAZ

6caz


Resolution: 1.65→43.391 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.9
RfactorNum. reflection% reflection
Rfree0.2078 1947 1.63 %
Rwork0.1822 --
obs0.1826 119355 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.84 Å2 / Biso mean: 33.0307 Å2 / Biso min: 13.45 Å2
Refinement stepCycle: final / Resolution: 1.65→43.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5368 0 137 642 6147
Biso mean--38.32 42.04 -
Num. residues----688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69120.28611100.23587732784291
1.6912-1.7370.23661370.2218483862099
1.737-1.78810.21721360.20185628698100
1.7881-1.84580.23681220.193884978619100
1.8458-1.91180.22781680.28461862999
1.9118-1.98830.21981160.19528465858199
1.9883-2.07880.21961610.18188467862899
2.0788-2.18840.20031730.17388429860299
2.1884-2.32550.211580.188408856698
2.3255-2.5050.20741290.18388417854698
2.505-2.75710.20671500.18778381853198
2.7571-3.15590.22231530.18728325847897
3.1559-3.97570.191310.17388320845197
3.9757-43.40630.19331030.17088461856497
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)
12.5931-0.05250.40512.4074-1.15426.1677-0.0558-0.09990.16070.4339-0.0294-0.2965-0.37960.35420.08810.2095-0.0482-0.07180.1464-0.00420.23520.912320.080834.7534
25.88930.56074.98553.3501-1.63248.1813-0.1062-0.29190.10020.43380.01280.0906-0.5004-0.3150.12510.18260.02390.02550.1321-0.02280.1849-9.712220.367137.6374
33.70450.40440.77146.1034-0.84775.3154-0.0156-0.1122-0.14750.2265-0.05340.08390.0421-0.23360.09580.1160.01770.02070.1245-0.02840.1083-6.637114.244132.3696
40.36080.72990.43553.841-0.02975.07890.07810.0166-0.20760.192-0.0789-0.02140.81310.00250.01310.25910.0014-0.02220.16630.00960.2596-5.26562.569533.2548
50.50480.1628-0.2321.77210.01654.20920.0102-0.0172-0.15220.2753-0.013-0.12150.5792-0.03710.00650.24010.0104-0.01680.17210.01350.2224-3.89255.152332.5751
65.8598-2.05-3.84155.8465.25637.168-0.10640.0584-0.3420.27580.0967-0.59430.1475-0.0057-0.01430.17630.0379-0.00710.26860.00470.29985.68156.801622.9116
79.4671-6.28322.68514.7384-3.30444.75530.01260.87330.5897-0.4792-0.2973-0.4891-0.23250.50090.29440.1985-0.0778-0.02780.33730.05360.27391.66518.601412.3999
82.73633.8326-2.48226.7186-3.03944.3196-0.09610.21060.3371-0.27820.0750.0491-0.4574-0.196-0.11490.22180.0163-0.05020.19950.01970.2829-16.835624.94699.894
93.60480.43890.72962.4999-0.47913.0932-0.16820.3640.3593-0.50040.07580.1315-0.2519-0.04240.09520.2455-0.0231-0.04180.18780.02840.1815-16.808120.12122.9777
102.6209-0.60281.4888.00780.2326.0234-0.05180.35690.0601-0.51920.0672-0.51740.10660.3629-0.00150.2439-0.04220.05730.21930.02810.1815-12.312613.29371.3417
113.03751.77884.05585.99843.49797.82290.25970.188-0.3148-0.05280.09140.10270.90890.0027-0.3490.2463-0.0277-0.02360.2198-0.04510.2391-18.735-0.94298.4953
122.24242.60062.68183.02842.96886.93460.0974-0.003-0.0310.2017-0.0333-0.05860.366-0.1422-0.11140.0951-0.00950.03190.1919-0.00960.1735-18.36647.267216.7061
130.7804-0.6210.04461.44060.69213.3179-0.00210.2799-0.1134-1.4229-0.1838-0.36740.4290.47330.04650.4683-0.02380.00450.3281-0.02820.1842-14.55467.7199-5.4764
142.4882-0.03550.88872.7216-0.5525.77270.00790.2686-0.1483-0.43350.1156-0.01260.40070.1702-0.09770.2214-0.0403-0.00510.2046-0.03480.1536-16.45395.69453.8011
156.51560.9386-1.48738.6871-5.92396.7699-0.21630.0843-0.3284-0.19460.41320.45570.2713-0.4163-0.24540.1469-0.03020.00730.253-0.01920.2479-26.17387.357915.1663
164.69975.10412.9525.65733.42954.1646-0.0359-0.76960.24760.4691-0.22340.0715-0.2393-0.43920.36110.2040.0937-0.02730.3835-0.06720.3168-22.143717.713827.0124
178.70214.13863.47846.12940.67056.83850.18530.121-0.4541-0.2728-0.0902-0.04190.5760.106-0.09440.29670.0540.0620.12470.00450.162-8.82537.31248.4929
184.38420.6094-0.37234.01480.46310.1087-0.24930.6044-0.1055-0.8227-0.01630.15370.2180.3386-0.00850.40050.0370.15010.38020.05080.1089-6.940344.6296-3.5999
194.0513-0.90672.173.2258-2.41782.53250.1120.0308-0.1515-0.35610.0660.29270.3549-0.0072-0.15910.2395-0.02530.01250.1452-0.01210.209-18.152240.55265.3185
205.0546-0.66110.79825.9821-0.84097.1432-0.0699-0.06050.2414-0.1683-0.0840.2942-0.0097-0.24930.1020.1467-0.0221-0.00540.0984-0.020.1422-13.327546.82177.5304
211.3508-0.20871.60881.7889-0.37853.4803-0.41570.07540.4313-0.1937-0.06540.0153-0.72230.0370.38760.31550.0032-0.0590.17260.01990.2706-12.170856.24137.3294
222.7461-0.92752.44212.2107-0.36364.954-0.33640.16630.4116-0.3481-0.0374-0.0598-0.46030.20230.34250.3029-0.0442-0.04230.17540.05880.2513-8.03156.16047.0089
234.58244.1194-2.69154.3643-3.47097.204-0.1526-0.3813-0.23930.0115-0.3504-0.75170.53940.90820.50620.21790.08820.0320.35180.05540.30123.580643.115121.8581
243.9466-1.01650.83982.33351.42974.7911-0.0979-0.3436-0.2770.54380.04420.00920.5254-0.14370.06110.3808-0.02220.09560.19980.05620.2151-12.186838.774139.4497
252.8563-0.53970.33363.9253-0.31516.521-0.1679-0.0729-0.00920.2070.0474-0.28560.21820.2610.13220.19550.0440.01310.1419-0.00410.168-4.105743.568636.5796
263.1161.43972.83868.24425.54248.6603-0.281-0.17170.213-0.01090.06940.1081-0.7479-0.09430.30240.30270.0486-0.01610.2362-0.05580.244-12.158162.143735.1893
271.26090.46891.05192.66290.71153.3915-0.1384-0.08130.02130.33650.0908-0.1899-0.14280.19930.0710.21840.037-0.00850.2036-0.04190.1761-8.915854.112936.6517
283.9675-1.45670.50345.00231.11594.6315-0.1130.1475-0.1538-0.0145-0.26040.43690.3397-0.76290.39550.2019-0.08020.0850.2957-0.03830.2253-23.365945.665423.6048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 25 )A-1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 41 )A26 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 66 )A42 - 66
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 90 )A67 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 139 )A91 - 139
6X-RAY DIFFRACTION6chain 'A' and (resid 140 through 148 )A140 - 148
7X-RAY DIFFRACTION7chain 'A' and (resid 149 through 170 )A149 - 170
8X-RAY DIFFRACTION8chain 'B' and (resid -1 through 11 )B-1 - 11
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 52 )B12 - 52
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 76 )B53 - 76
11X-RAY DIFFRACTION11chain 'B' and (resid 77 through 90 )B77 - 90
12X-RAY DIFFRACTION12chain 'B' and (resid 91 through 105 )B91 - 105
13X-RAY DIFFRACTION13chain 'B' and (resid 106 through 117 )B106 - 117
14X-RAY DIFFRACTION14chain 'B' and (resid 118 through 139 )B118 - 139
15X-RAY DIFFRACTION15chain 'B' and (resid 140 through 148 )B140 - 148
16X-RAY DIFFRACTION16chain 'B' and (resid 149 through 170 )B149 - 170
17X-RAY DIFFRACTION17chain 'C' and (resid -1 through 11 )C-1 - 11
18X-RAY DIFFRACTION18chain 'C' and (resid 12 through 25 )C12 - 25
19X-RAY DIFFRACTION19chain 'C' and (resid 26 through 41 )C26 - 41
20X-RAY DIFFRACTION20chain 'C' and (resid 42 through 66 )C42 - 66
21X-RAY DIFFRACTION21chain 'C' and (resid 67 through 117 )C67 - 117
22X-RAY DIFFRACTION22chain 'C' and (resid 118 through 148 )C118 - 148
23X-RAY DIFFRACTION23chain 'C' and (resid 149 through 170 )C149 - 170
24X-RAY DIFFRACTION24chain 'D' and (resid -1 through 25 )D-1 - 25
25X-RAY DIFFRACTION25chain 'D' and (resid 26 through 76 )D26 - 76
26X-RAY DIFFRACTION26chain 'D' and (resid 77 through 89 )D77 - 89
27X-RAY DIFFRACTION27chain 'D' and (resid 90 through 139 )D90 - 139
28X-RAY DIFFRACTION28chain 'D' and (resid 140 through 170 )D140 - 170

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