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- PDB-6il2: K4U complex structure of peptide deformylase from Xanthomonas ory... -

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Basic information

Entry
Database: PDB / ID: 6il2
TitleK4U 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
: / L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE / Peptide deformylase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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
Revision 1.2Oct 16, 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)19,2135
Polymers18,6511
Non-polymers5614
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-9 kcal/mol
Surface area8000 Å2
Unit cell
Length a, b, c (Å)58.531, 58.531, 266.212
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85) (bacteria)
Strain: KACC10331 / KXO85 / 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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-LHY / L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE


Mass: 224.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.76 Å3/Da / Density % sol: 67.26 % / Mosaicity: 0.887 °
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: 2.4→50 Å / Num. obs: 11239 / % possible obs: 98.3 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.042 / Rrim(I) all: 0.189 / Χ2: 7.711 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4410.50.4855390.5460.1480.5091.64698.2
2.44-2.4910.80.4855240.7680.1440.5081.8297.6
2.49-2.5310.90.4635610.7010.1390.4851.85297.7
2.53-2.5911.20.4295110.8250.1230.4472.0497.7
2.59-2.64120.3975430.9110.1110.4132.0298
2.64-2.712.10.3845490.8940.1060.42.22598.9
2.7-2.7712.90.3465460.9460.0930.3592.32698.6
2.77-2.85130.3325340.9320.0880.3442.70898.2
2.85-2.9314.20.3015630.960.0750.3113.01198.8
2.93-3.02150.2815340.9670.0690.2893.25298.3
3.02-3.13150.2625460.970.0640.273.68198.6
3.13-3.2615.90.2365830.9860.0550.2435.00998.8
3.26-3.4117.30.2195440.9830.0490.2246.5498.4
3.41-3.5818.30.2015610.9880.0440.2067.84398.6
3.58-3.8120.30.1915610.9920.040.19510.41598.9
3.81-4.120.10.1775710.9870.0380.18112.52499.1
4.1-4.52210.1615900.9930.0340.16513.81598.8
4.52-5.1720.10.1525880.9930.0320.15514.93299
5.17-6.51210.1446130.9960.030.14711.94598.2
6.51-5020.60.126780.9960.0260.12315.43695.5

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Processing

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

5e5d


Resolution: 2.41→49.9 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.733 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.195
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 529 4.7 %RANDOM
Rwork0.1919 ---
obs0.1939 10700 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.53 Å2 / Biso mean: 33.34 Å2 / Biso min: 18.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.41→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 18 19 1258
Biso mean--43.31 32.38 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191263
X-RAY DIFFRACTIONr_bond_other_d0.0020.021174
X-RAY DIFFRACTIONr_angle_refined_deg2.0721.981710
X-RAY DIFFRACTIONr_angle_other_deg1.10432697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.955155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67822.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67115197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8451513
X-RAY DIFFRACTIONr_chiral_restr0.1250.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211425
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02278
LS refinement shellResolution: 2.407→2.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 39 -
Rwork0.29 749 -
all-788 -
obs--96.92 %

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