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- PDB-6jf8: K4U bound crystal structure of class I type b peptide deformylase... -

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Basic information

Entry
Database: PDB / ID: 6jf8
TitleK4U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii
ComponentsPeptide 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
L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, I.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To be published
Title: K4U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii
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_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)71,69212
Polymers70,5334
Non-polymers1,1588
Water3,495194
1
A: Peptide deformylase
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8466
Polymers35,2672
Non-polymers5794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-18 kcal/mol
Surface area13340 Å2
MethodPISA
2
C: Peptide deformylase
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8466
Polymers35,2672
Non-polymers5794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-18 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.158, 40.034, 111.051
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptide deformylase / PDF / Polypeptide deformylase


Mass: 17633.338 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: K0420859 / Gene: def, C3415_07350, IX87_00730 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0E1FIJ3, UniProt: A0A6H2UJ23*PLUS, peptide deformylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-LHY / L-[(N-HYDROXYAMINO)CARBONYL]PHENYLALANINE


Mass: 224.213 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.24 Å3/Da / Density % sol: 45.15 % / Mosaicity: 0.467 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 6.5
Details: 0.2 M Calcium acetate hydrate, 0.1 M sodium cacodylate trihydrate pH 6.5, 18% (w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 68073 / % possible obs: 98.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.059 / Rrim(I) all: 0.133 / Χ2: 9.446 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.733.70.56330710.8410.3270.6551.92888.5
1.73-1.764.10.47432110.8970.2570.5422.16395.5
1.76-1.794.70.39434200.9530.1940.442.50299.7
1.79-1.834.70.34234290.9520.1670.3822.80599.8
1.83-1.874.70.27434060.9530.1340.3063.25899.9
1.87-1.914.70.24834370.9620.1210.2773.89100
1.91-1.964.80.21334040.9720.1040.2384.04399.9
1.96-2.024.80.18134360.9660.0890.2025.134100
2.02-2.074.80.16134380.9780.0790.185.324100
2.07-2.144.80.14334570.980.070.165.99899.9
2.14-2.224.80.13234440.9860.0650.1486.77499.9
2.22-2.314.90.12534100.9770.0620.147.769100
2.31-2.414.90.11934390.9790.0580.1338.287100
2.41-2.544.90.11234720.9830.0550.1269.361100
2.54-2.74.90.1134500.980.0540.12310.95100
2.7-2.914.90.10734730.980.0520.1213.416100
2.91-3.24.90.11134550.9840.0540.12418.068100
3.2-3.664.80.11235000.9820.0550.12523.56599.9
3.66-4.614.60.09434680.9850.0490.10623.01799
4.61-504.30.09432530.9820.050.10728.57389.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JES

6jes


Resolution: 1.7→49.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.978 / SU ML: 0.065 / SU R Cruickshank DPI: 0.1016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 3406 5 %RANDOM
Rwork0.1715 ---
obs0.1735 64656 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.42 Å2 / Biso mean: 25.035 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.7→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 68 194 5112
Biso mean--29.85 27.96 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0195001
X-RAY DIFFRACTIONr_bond_other_d0.0020.024699
X-RAY DIFFRACTIONr_angle_refined_deg2.1081.9886796
X-RAY DIFFRACTIONr_angle_other_deg1.201310888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4425629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16624.884215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96815827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6581531
X-RAY DIFFRACTIONr_chiral_restr0.1310.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215594
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02941
LS refinement shellResolution: 1.702→1.747 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 205 -
Rwork0.23 4145 -
all-4350 -
obs--86.26 %

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