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- PDB-5e5d: Native structure of Xoo1075, a peptide deformylase from Xanthomon... -

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Basic information

Entry
Database: PDB / ID: 5e5d
TitleNative structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv. oryzae
ComponentsPeptide deformylase
KeywordsHYDROLASE / peptide deformylase / metal binding protein
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
: / Peptide deformylase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae KACC10331 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNgo, H.P.T. / Kang, L.W.
CitationJournal: To Be Published
Title: Native structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv. oryzae
Authors: Ngo, H.P.T. / Kang, L.W.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionOct 12, 2016ID: 3DLD
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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
Revision 1.2Mar 5, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details

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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)24,1684
Polymers23,8301
Non-polymers3373
Water2,090116
1
A: Peptide deformylase
hetero molecules

A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3358
Polymers47,6612
Non-polymers6746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2510 Å2
ΔGint-50 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.968, 58.968, 266.285
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-399-

HOH

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 23830.295 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.8 Å3/Da / Density % sol: 56.14 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 9011 / % possible obs: 96.9 % / Redundancy: 9.6 % / Net I/σ(I): 22.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 6.6 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sv2

1sv2


Resolution: 2.6→30.4 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.047 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 422 4.7 %RANDOM
Rwork0.18732 ---
obs0.18981 8502 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.562 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.6→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 3 116 1454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9661855
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9855169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44622.89969
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68315215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9121514
X-RAY DIFFRACTIONr_chiral_restr0.1550.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211078
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_it2.2592.928678
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4094.373847
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3973.158695
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.89725.1772221
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: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 29 -
Rwork0.221 606 -
obs--97.24 %

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