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- PDB-6il0: K3U complex structure of peptide deformylase from Xanthomonas ory... -

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Basic information

Entry
Database: PDB / ID: 6il0
TitleK3U complex structure of peptide deformylase from Xanthomonas oryzae pv. oryzae
ComponentsPeptide 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
Chem-K3U / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae KACC10331 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLee, I.H. / Kang, L.W.
CitationJournal: To be published
Title: FBIs complex structure of peptide deformylase from Xanthomonas oryzae pv. oryzae
Authors: Lee, I.H. / Kang, L.W.
History
DepositionOct 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)19,4445
Polymers18,9011
Non-polymers5424
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area8180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.682, 58.682, 265.531
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 18901.410 Da / Num. of mol.: 1 / Fragment: UNP residues 42-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae KACC10331 (bacteria)
Strain: KACC10331 / Gene: def, XOO1075 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5H3Z2, peptide deformylase
#2: Chemical ChemComp-K3U / S-(2-oxo-2-phenylethyl) (2R)-2-benzyl-4,4,4-trifluorobutanethioate


Mass: 366.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17F3O2S
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.69 Å3/Da / Density % sol: 66.7 % / Mosaicity: 0.968 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 7.5
Details: 0.05M cadmium sulfate, 0.1M HEPES pH 7.5, 2.0M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 20671 / % possible obs: 96 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.043 / Rrim(I) all: 0.14 / Χ2: 10.026 / Net I/σ(I): 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.964.80.4999650.4460.2180.5492.86991.6
1.96-25.50.4579480.5440.190.4982.85192.4
2-2.045.80.4089670.6710.1610.4422.99192.4
2.04-2.0860.3779750.7440.1480.4083.21194
2.08-2.126.40.3449770.8370.1280.3693.75594.7
2.12-2.176.70.3049870.8810.1120.3263.99594.3
2.17-2.236.90.2729850.9050.1020.2934.28794.7
2.23-2.2970.2410040.9190.0880.2574.4895.5
2.29-2.367.10.21510280.9390.0790.2314.5997.1
2.36-2.437.50.20710190.9420.0740.2214.68296.2
2.43-2.527.60.18110200.9660.0630.1935.29397.9
2.52-2.627.90.16210260.970.0560.1735.91597.1
2.62-2.748.20.15910670.970.0550.1697.01698.3
2.74-2.888.70.14710420.9810.0490.1568.1598.6
2.88-3.069.20.14510690.9740.0480.15310.64998.7
3.06-3.39.80.13810790.9860.0430.14513.17798.7
3.3-3.6310.40.13810910.9860.0430.14517.72699.3
3.63-4.1610.80.12410980.990.0380.13121.19298.9
4.16-5.2410.90.09311200.9920.0290.09817.1597.4
5.24-5013.50.08112040.9930.0230.08417.5493.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E5D

5e5d


Resolution: 1.93→49.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.802 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.119
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 1066 5.2 %RANDOM
Rwork0.1953 ---
obs0.1971 19579 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.52 Å2 / Biso mean: 28.001 Å2 / Biso min: 15.67 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.93→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 28 40 1318
Biso mean--55.6 30.63 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191304
X-RAY DIFFRACTIONr_bond_other_d0.0020.021203
X-RAY DIFFRACTIONr_angle_refined_deg2.3061.9881767
X-RAY DIFFRACTIONr_angle_other_deg1.10132769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1315158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06222.74262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25615201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7781513
X-RAY DIFFRACTIONr_chiral_restr0.140.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02286
LS refinement shellResolution: 1.934→1.984 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 73 -
Rwork0.257 1348 -
all-1421 -
obs--92.63 %

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