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- PDB-2okl: Crystal structure of Peptide Deformylase 2 with actinonin from Ba... -

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Basic information

Entry
Database: PDB / ID: 2okl
TitleCrystal structure of Peptide Deformylase 2 with actinonin from Bacillus cereus
ComponentsPeptide deformylase 2
KeywordsHYDROLASE
Function / homology
Function and homology information


co-translational protein modification / N-terminal protein amino acid modification / peptidyl-methionine modification / 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 / CITRIC ACID / Peptide deformylase 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKim, E.E.
CitationJournal: J.Biochem.Mol.Biol. / Year: 2007
Title: Characterization of Peptide Deformylase2 from B. cereus
Authors: Park, J.K. / Kim, K.H. / Moon, J.H. / Kim, E.E.
History
DepositionJan 17, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide deformylase 2
B: Peptide deformylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1429
Polymers41,2772
Non-polymers1,8657
Water6,053336
1
A: Peptide deformylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6675
Polymers20,6391
Non-polymers1,0294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide deformylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4754
Polymers20,6391
Non-polymers8363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.447, 69.447, 294.412
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-684-

HOH

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Components

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


Mass: 20638.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: def2 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q819K2, peptide deformylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: antitumor, antibiotic*YM
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Na-Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11
SYNCHROTRONPAL/PLS 6B21.2823, 1.2693, 1.2828
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDMar 9, 2005wiggler
BRUKER PROTEUM 3002CCDJan 19, 2005mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1wigglerSINGLE WAVELENGTHMx-ray1
2Double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.28231
31.26931
41.28281
ReflectionResolution: 1.65→50 Å / Num. all: 52252 / Num. obs: 52252 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 40.3
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 1.54 / Num. unique all: 3965 / % possible all: 78.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 321044.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2254 5 %RANDOM
Rwork0.228 ---
obs0.228 45204 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4366 Å2 / ksol: 0.363823 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å21.5 Å20 Å2
2--3.88 Å20 Å2
3----7.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 123 336 3345
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it2.331.5
X-RAY DIFFRACTIONc_mcangle_it3.692
X-RAY DIFFRACTIONc_scbond_it3.872
X-RAY DIFFRACTIONc_scangle_it6.022.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 324 4.7 %
Rwork0.326 6575 -
obs--89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4cit.paramcit.top
X-RAY DIFFRACTION5bb2.parambb2.top

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