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- PDB-6iky: K2U complex structure of peptide deformylase from Xanthomonas ory... -

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Basic information

Entry
Database: PDB / ID: 6iky
TitleK2U 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-K2U / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae KACC10331 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_asym_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_asym_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_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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1445
Polymers18,6511
Non-polymers4924
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-13 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.754, 58.754, 267.674
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: 18651.156 Da / Num. of mol.: 1 / Fragment: UNP residues 42-208
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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-K2U / (3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid


Mass: 316.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.79 Å3/Da / Density % sol: 67.51 % / Mosaicity: 1.107 °
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: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22054 / % possible obs: 95.7 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.029 / Rrim(I) all: 0.099 / Χ2: 2.919 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.937.10.4939920.4150.1750.5261.42891.4
1.93-1.977.30.45410210.720.1570.4831.47789.2
1.97-2.017.60.41810310.8240.140.4421.58894.7
2.01-2.058.10.37810290.8550.1220.3991.71691.2
2.05-2.098.20.36510340.890.1180.3851.79593.4
2.09-2.148.70.30310270.9390.0950.3191.86991.9
2.14-2.198.40.2810460.9520.0890.2951.92393.6
2.19-2.258.60.24810790.9680.0780.2612.03495.9
2.25-2.328.70.22810810.9720.0710.242.14695.7
2.32-2.3990.21510750.9750.0660.2262.08595.6
2.39-2.4890.1911060.9810.0590.22.19196.2
2.48-2.589.30.16710910.9870.0510.1762.40297.2
2.58-2.79.50.14811280.990.0450.1562.67596.8
2.7-2.849.80.13511210.9920.0410.1422.9298.9
2.84-3.0210.30.11611350.9930.0350.1223.27798.3
3.02-3.2510.40.10411580.9950.0310.1093.95899.4
3.25-3.5810.80.08711530.9960.0270.0914.55299.2
3.58-4.0910.70.07611960.9960.0240.085.0499.4
4.09-5.1611.60.06112130.9980.0180.0644.4798.4
5.16-5013.50.05913380.9980.0170.0613.91997

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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: 1.9→47.56 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.738 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.116
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 1041 4.8 %RANDOM
Rwork0.2032 ---
obs0.2049 20815 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.74 Å2 / Biso mean: 29.626 Å2 / Biso min: 17.13 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.9→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 25 26 1303
Biso mean--56.85 29.15 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191303
X-RAY DIFFRACTIONr_bond_other_d0.0020.021209
X-RAY DIFFRACTIONr_angle_refined_deg2.2421.9831763
X-RAY DIFFRACTIONr_angle_other_deg1.09132784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0125158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63222.85763
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00215202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0471513
X-RAY DIFFRACTIONr_chiral_restr0.1420.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 75 -
Rwork0.287 1409 -
all-1484 -
obs--91.89 %

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