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- PDB-6jf6: Met-ala-ser bound crystal structure of class I type b peptide def... -

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Basic information

Entry
Database: PDB / ID: 6jf6
TitleMet-ala-ser bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii
Components
  • MET-ALA-SER
  • Peptide deformylase
KeywordsHYDROLASE / peptide deformylase
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
Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsJung, K.H. / Ho, T.H. / Lee, I.H. / Kang, L.W.
CitationJournal: To be published
Title: Met-ala-ser bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii
Authors: Jung, K.H. / Ho, T.H. / Lee, I.H. / Kang, L.W.
History
DepositionFeb 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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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
E: MET-ALA-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6279
Polymers71,3665
Non-polymers2624
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-198 kcal/mol
Surface area26890 Å2
Unit cell
Length a, b, c (Å)71.370, 39.347, 110.353
Angle α, β, γ (deg.)90.000, 89.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptide deformylase / PDF / Polypeptide deformylase


Mass: 17764.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: def, C3415_07350, IX87_00730 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0E1FIJ3, UniProt: A0A6H2UJ23*PLUS, peptide deformylase
#2: Protein/peptide MET-ALA-SER


Mass: 307.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.62 % / Mosaicity: 0.596 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 6.5
Details: 0.2 M Calcium acetate hydrate, 0.1 M sodium cacodylate trihydrate pH 6.5, 18% (w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.4856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4856 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 26193 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.062 / Rrim(I) all: 0.159 / Χ2: 1.436 / Net I/σ(I): 4.4 / Num. measured all: 168949
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.395.60.48412750.920.220.5330.69999.2
2.39-2.4360.45412820.9320.20.4970.6899.4
2.43-2.486.50.42513220.9220.1770.4610.741100
2.48-2.536.70.37512760.9480.1540.4060.81199.9
2.53-2.596.70.3412820.9580.140.3680.86199.8
2.59-2.656.60.33213440.9620.1380.360.84299.9
2.65-2.716.70.30412580.9630.1260.3290.94999.8
2.71-2.796.60.27113000.9680.1130.2941.02799.8
2.79-2.876.50.2512860.970.1030.271.14199.3
2.87-2.9660.2312900.9750.1020.2521.224100
2.96-3.076.10.21713240.9780.0950.2381.265100
3.07-3.196.90.1812870.9870.0740.1951.48100
3.19-3.336.90.17213220.9890.0710.1861.662100
3.33-3.516.70.15813000.9860.0660.1721.829100
3.51-3.736.70.14613170.9830.0610.1591.959100
3.73-4.026.30.13213440.9880.0570.1452.254100
4.02-4.425.90.12313160.9880.0560.1352.401100
4.42-5.066.80.11413330.9870.0470.1242.37100
5.06-6.376.70.11113300.9890.0470.1211.85499.7
6.37-5060.11214050.9860.050.1232.44499.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JES

6jes


Resolution: 2.35→49.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.888 / SU B: 11.389 / SU ML: 0.265 / SU R Cruickshank DPI: 0.5102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.51 / ESU R Free: 0.313
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2916 1397 5.4 %RANDOM
Rwork0.2101 ---
obs0.2144 24673 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.37 Å2 / Biso mean: 47.539 Å2 / Biso min: 23.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.35→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 4 99 4961
Biso mean--51.6 42.41 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194942
X-RAY DIFFRACTIONr_bond_other_d0.0020.024686
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9756709
X-RAY DIFFRACTIONr_angle_other_deg1.001310870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.94324.93215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97215843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5811531
X-RAY DIFFRACTIONr_chiral_restr0.0970.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215479
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02900
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 94 -
Rwork0.296 1780 -
all-1874 -
obs--98.58 %

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