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- PDB-6jfa: Met-Ala-Ser bound crystal structure of class I type b peptide def... -

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Basic information

Entry
Database: PDB / ID: 6jfa
TitleMet-Ala-Ser bound crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa
Components
  • MET-ALA-SER
  • Peptide 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
NICKEL (II) ION / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: Met-Ala-Ser bound crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa
Authors: Lee, I.H. / Ho, T.H. / Kang, L.W.
History
DepositionFeb 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: 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_asym_id / _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.ptnr3_auth_asym_id / _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.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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

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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: MET-ALA-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9156
Polymers38,7393
Non-polymers1763
Water1,910106
1
A: Peptide deformylase
C: MET-ALA-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5823
Polymers19,5232
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-16 kcal/mol
Surface area8300 Å2
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3333
Polymers19,2161
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.815, 122.826, 143.978
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 19215.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAE0831 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1C7BES9, UniProt: A0A071LDC0*PLUS, peptide deformylase
#2: Protein/peptide MET-ALA-SER


Mass: 307.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 8
Details: 0.03 M CaCl2, 0.03 M MgCl2, 0.1 M Sodium Hepes: MOPS pH 8.0, 10.0% (v/v) MPD, 10.0% (w/v) P1k, 10.0% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 29554 / % possible obs: 97.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.043 / Rrim(I) all: 0.108 / Χ2: 5.928 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.962.90.38413800.7450.2360.4551.1693.3
1.96-23.40.39714270.8430.2330.4631.16895.5
2-2.0440.38614870.8570.2080.4411.35997.9
2.04-2.084.10.36314440.9450.1940.4141.41298.5
2.08-2.124.30.31514900.9220.1630.3571.57198.5
2.12-2.174.10.27514630.9510.1430.3111.61397.8
2.17-2.233.10.21513400.9620.1210.2482.17489.5
2.23-2.295.40.51414400.8510.2120.55723.64195.6
2.29-2.363.80.17614210.9850.0910.21.97994.4
2.36-2.434.60.18614770.960.090.2082.09498.4
2.43-2.524.90.16615040.9850.0780.1842.3598.8
2.52-2.625.20.1514880.9910.0690.1652.62699.3
2.62-2.745.40.1315020.9940.0580.1432.99899.5
2.74-2.885.60.11714850.9940.0510.1284.00699.4
2.88-3.065.90.11315210.9940.0480.1224.87499.5
3.06-3.36.10.10315310.9940.0430.1126.71699.7
3.3-3.6360.10715400.9930.0450.11610.43199.4
3.63-4.1660.09215230.9930.040.112.09299.2
4.16-5.246.30.05915380.9970.0250.0647.70698.8
5.24-506.40.05915530.9940.0250.0648.84892.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JF9

6jf9


Resolution: 1.93→31.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.458 / SU ML: 0.186 / SU R Cruickshank DPI: 0.1808 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.175
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2884 1406 4.8 %RANDOM
Rwork0.2358 ---
obs0.2383 28130 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.94 Å2 / Biso mean: 45.975 Å2 / Biso min: 23.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.93→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 3 106 2635
Biso mean--61.97 48.08 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132579
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172456
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.6453488
X-RAY DIFFRACTIONr_angle_other_deg1.4831.5735684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82520.53151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89315441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4781528
X-RAY DIFFRACTIONr_chiral_restr0.0840.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
LS refinement shellResolution: 1.931→1.981 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 104 -
Rwork0.501 1970 -
all-2074 -
obs--93.68 %

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