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- PDB-5cvk: Structure of Xoo1075, a peptide deformyase from Xanthomonas oryza... -

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Basic information

Entry
Database: PDB / ID: 5cvk
TitleStructure of Xoo1075, a peptide deformyase from Xanthomonas oryzae pv. oryze, in complex with fragment 493
ComponentsPeptide deformylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / peptide deformylase / xanthomonas / fragment / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / co-translational protein modification / 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-56E / ACETATE ION / : / Peptide deformylase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae KACC10331 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsNgo, H.P.T. / Kang, L.W.
CitationJournal: To Be Published
Title: Structure of Xoo1075, a peptide deformyase from Xanthomonas oryzae pv.oryze, in complex with fragment 493
Authors: Ngo, H.P.T. / Kang, L.W.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_alt_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_alt_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_symmetry

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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)19,9699
Polymers19,0981
Non-polymers8718
Water3,225179
1
A: Peptide deformylase
hetero molecules

A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,93818
Polymers38,1952
Non-polymers1,74316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3890 Å2
ΔGint-105 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.002, 59.002, 264.653
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 19097.656 Da / Num. of mol.: 1 / Fragment: UNP residues 42-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae KACC10331 (bacteria)
Strain: KACC10331 / Gene: def, XOO1075 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5H3Z2, peptide deformylase

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Non-polymers , 5 types, 187 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-56E / ethyl N-[(5-methylthiophen-3-yl)carbonyl]glycinate


Mass: 227.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO3S
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M Cadmium sulfate, 0.1M HEPES, 2.0M Sodium acetate trihydrate, pH 7.5
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19166 / % possible obs: 97.5 % / Redundancy: 7.9 % / Net I/σ(I): 21.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementResolution: 2.1→26.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.284 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22387 832 5 %RANDOM
Rwork0.17645 ---
obs0.17873 15907 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.993 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.1→26.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 25 179 1527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191378
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.9831870
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16323.08868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84415211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0431513
X-RAY DIFFRACTIONr_chiral_restr0.1490.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211092
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.12.205676
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8733.274842
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2862.531701
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.59719.5912213
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 59 -
Rwork0.181 1069 -
obs--94.87 %

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