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- PDB-4wxk: Crystal structure of a peptide deformylase from Haemophilus influenzae -

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Basic information

Entry
Database: PDB / ID: 4wxk
TitleCrystal structure of a peptide deformylase from Haemophilus influenzae
ComponentsPeptide deformylase
KeywordsHYDROLASE / peptide deformylase
Function / homology
Function and homology information


co-translational protein modification / 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
NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesHaemophilus influenzae 86-028NP (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKishor, C. / Addlagatta, A.
CitationJournal: To Be Published
Title: Crystal structure of a peptide deformylase from Haemophilus influenzae
Authors: Kishor, C. / Addlagatta, A.
History
DepositionNov 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: 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_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_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide deformylase
B: Peptide deformylase
C: Peptide deformylase
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,02813
Polymers76,3334
Non-polymers6959
Water5,405300
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2343
Polymers19,0831
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-11 kcal/mol
Surface area8560 Å2
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2343
Polymers19,0831
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-11 kcal/mol
Surface area8690 Å2
MethodPISA
3
C: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2343
Polymers19,0831
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area9080 Å2
MethodPISA
4
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3264
Polymers19,0831
Non-polymers2433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-11 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.036, 80.961, 98.586
Angle α, β, γ (deg.)90.00, 97.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptide deformylase / PDF / Polypeptide deformylase


Mass: 19083.139 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae 86-028NP (bacteria)
Gene: def, NTHI0725 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QMV6, peptide deformylase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20-25% PEG 3350, 0.1M HEPES pH 7.0, 2% glycerol / PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→25.37 Å / Num. obs: 39520 / % possible obs: 97.69 % / Redundancy: 3.6 % / Net I/σ(I): 11.67

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data reduction
DENZOdata scaling
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G2A

1g2a


Resolution: 2.05→25.37 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.98 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22161 1978 5 %RANDOM
Rwork0.16078 ---
obs0.16382 37541 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.268 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.05→25.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5234 0 34 300 5568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195425
X-RAY DIFFRACTIONr_bond_other_d0.0010.025496
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.9997343
X-RAY DIFFRACTIONr_angle_other_deg0.87312695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.12725.317252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.396151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.541535
X-RAY DIFFRACTIONr_chiral_restr0.1130.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021099
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.045→2.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 122 -
Rwork0.158 2156 -
obs--76.83 %

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