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- PDB-6caz: Crystal structure of a peptide deformylase from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 6caz
TitleCrystal structure of a peptide deformylase from Legionella pneumophila
ComponentsPeptide deformylase
KeywordsHYDROLASE / NIAID / structural genomics / metalloenzyme / Legionnaires' disease / Legionellosis / Gram-negative bacteria / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5784
Polymers20,2891
Non-polymers2893
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.210, 50.900, 105.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 20288.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: def, lpg2595 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSC4, peptide deformylase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16.5 mg/mL LepnA.00882.a.B1.P38390 against Morpheus screen condition F1 10% PEG 10,000, 20% PEG 550 MME, 0.02 M each monosaccharide (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N- ...Details: 16.5 mg/mL LepnA.00882.a.B1.P38390 against Morpheus screen condition F1 10% PEG 10,000, 20% PEG 550 MME, 0.02 M each monosaccharide (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine), 0.1 M MES/imidazole pH 6.5, crystal tracking ID 297178f1, ugh2-12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→45.829 Å / Num. obs: 33486 / % possible obs: 99.3 % / Redundancy: 10.049 % / Biso Wilson estimate: 15.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.037 / Χ2: 1.021 / Net I/σ(I): 33.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.546.8250.3924.7423680.8770.42496.3
1.54-1.587.1550.2956.123330.940.31897.2
1.58-1.637.4380.2327.6322840.970.24998.7
1.63-1.687.8120.1929.2422270.9840.20598.3
1.68-1.738.1330.15911.3722040.9870.169100
1.73-1.798.5110.13213.8121010.9910.1499.7
1.79-1.868.8950.10816.4620590.9950.114100
1.86-1.949.2940.08920.919810.9960.095100
1.94-2.029.6260.0727.7719200.9980.074100
2.02-2.12100.05635.3918450.9990.059100
2.12-2.2410.340.04940.1817210.9990.05299.9
2.24-2.3710.60.04347.3616480.9990.04599.9
2.37-2.5411.2260.03853.3715540.9990.0499.9
2.54-2.7411.5910.03558.4146110.037100
2.74-312.1970.03165.94133810.03399.8
3-3.3513.1270.02974.06122710.0399.8
3.35-3.8715.3530.02788.21109210.02899.9
3.87-4.7419.5730.027102.8993410.02899.8
4.74-6.7119.8820.026103.6174010.027100
6.71-45.82917.7530.02699.874490.9990.02799.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(1.13_2998)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w3t

2w3t


Resolution: 1.5→45.829 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.22
RfactorNum. reflection% reflection
Rfree0.1929 1655 4.94 %
Rwork0.166 --
obs0.1673 33481 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.72 Å2 / Biso mean: 24.1449 Å2 / Biso min: 8.68 Å2
Refinement stepCycle: final / Resolution: 1.5→45.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 14 276 1612
Biso mean--16.24 36.14 -
Num. residues----169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4999-1.54410.21811400.22032523266397
1.5441-1.59390.2161190.18392577269697
1.5939-1.65090.17091380.17332588272699
1.6509-1.7170.2031310.16942607273899
1.717-1.79510.21011490.166725982747100
1.7951-1.88970.19761290.169226742803100
1.8897-2.00810.2021450.170126542799100
2.0081-2.16320.16921460.163426492795100
2.1632-2.38090.18811460.161126622808100
2.3809-2.72540.19431340.169527032837100
2.7254-3.43350.20381420.171927202862100
3.4335-45.85080.1851360.153128713007100
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)
10.0172-0.18150.12613.2296-0.30676.51380.17330.02530.55990.26280.13380.6607-0.4015-0.46-0.34180.14980.03850.05190.14350.010.1919-4.183514.093218.4155
21.0720.5728-0.79472.9945-0.9852.71320.0539-0.01270.02780.19180.17330.2251-0.0624-0.2854-0.17010.1030.0214-0.00930.12520.02850.1121-3.35353.377220.7349
33.22471.0823-0.6171.3625-1.87775.3781-0.09210.1094-0.3525-0.47710.01270.69410.478-0.8614-0.31340.2796-0.1769-0.16270.43680.11020.3718-14.481-3.836810.2403
40.80110.1224-0.11360.7787-0.96232.5253-0.02290.0324-0.1112-0.28460.0541-0.0520.63260.0118-0.00510.23110.0075-0.00730.1092-0.00380.11891.1182-1.95318.2443
51.53280.3909-0.33581.1366-1.02312.09180.00210.0815-0.1626-0.31490.0471-0.02040.42840.0052-0.03320.18340.0157-0.01270.08930.0020.11752.41310.12648.7735
67.1488-3.5448-4.91325.10792.94515.53980.30190.160.5588-0.1144-0.1405-0.0731-0.501-0.2174-0.17670.20250.02450.00230.13380.01950.1335-0.324222.6636.3805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 11 )A2 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 61 )A12 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 70 )A62 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 117 )A71 - 117
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 148 )A118 - 148
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 170 )A149 - 170

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