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- PDB-6jfc: Actinonin bound crystal structure of class I type b peptide defor... -

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Basic information

Entry
Database: PDB / ID: 6jfc
TitleActinonin bound crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa
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
ACTINONIN / NICKEL (II) ION / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: Actinonin 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,1266
Polymers38,2382
Non-polymers8884
Water88349
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5633
Polymers19,1191
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-8 kcal/mol
Surface area8700 Å2
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5633
Polymers19,1191
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-8 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.020, 122.634, 148.142
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


Mass: 19118.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1C7BES9, UniProt: A0A071LDC0*PLUS, peptide deformylase
#2: Chemical ChemComp-BB2 / ACTINONIN / 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE


Mass: 385.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H35N3O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antitumor, antibiotic*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.76 Å3/Da / Density % sol: 55.36 %
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: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 25281 / % possible obs: 97.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.089 / Rrim(I) all: 0.186 / Χ2: 9.704 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.04-2.084.20.48111950.7890.2690.5552.36594.5
2.08-2.114.40.44712380.7640.2470.5152.60295.7
2.11-2.154.50.41412370.7750.2290.4772.8397.7
2.15-2.24.60.3912350.7940.2170.453.33495.7
2.2-2.254.60.35312720.8530.1990.4093.56198
2.25-2.34.70.31112390.8850.1740.3593.91499.1
2.3-2.354.80.30612480.8570.1650.354.44697.2
2.35-2.424.80.28412780.8620.1550.3264.18998.2
2.42-2.494.90.2512690.9050.1360.2874.96198.5
2.49-2.574.90.22612750.9230.120.2585.90398.7
2.57-2.6650.21712670.9330.1140.2466.88398.6
2.66-2.775.10.19912760.9540.1050.2277.47798.3
2.77-2.895.10.18412930.9470.0940.20810.04799.4
2.89-3.055.20.17712630.9570.090.19911.0298.4
3.05-3.245.20.16213030.9590.0840.18312.52498.3
3.24-3.495.30.15712650.950.080.17716.34697.8
3.49-3.8450.15312960.950.0830.17521.09197.2
3.84-4.394.50.14312660.9530.0810.16623.57395.2
4.39-5.544.50.13312760.9320.0790.15622.63994.7
5.54-504.70.11812900.950.0670.13620.1990.9

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Processing

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

6jf9


Resolution: 2.04→49.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.956 / SU ML: 0.132 / SU R Cruickshank DPI: 0.1883 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.174
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 1228 4.9 %RANDOM
Rwork0.203 ---
obs0.2053 24023 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.16 Å2 / Biso mean: 41.91 Å2 / Biso min: 21.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.04→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 56 49 2638
Biso mean--71.41 36.91 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192642
X-RAY DIFFRACTIONr_bond_other_d0.0020.022513
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9993571
X-RAY DIFFRACTIONr_angle_other_deg1.09235822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9045317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87123.095126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15115440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8091527
X-RAY DIFFRACTIONr_chiral_restr0.1240.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212913
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02538
LS refinement shellResolution: 2.041→2.094 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 97 -
Rwork0.302 1685 -
all-1782 -
obs--93.59 %

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