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- PDB-5j46: Crystal structure of a Peptide Deformylase from Burkholderia mult... -

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Basic information

Entry
Database: PDB / ID: 5j46
TitleCrystal structure of a Peptide Deformylase from Burkholderia multivorans
ComponentsPeptide deformylase
KeywordsHYDROLASE / SSGCID / Peptide deformylase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
Peptide deformylase 1
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a Peptide Deformylase from Burkholderia multivorans
Authors: Potts, K.T. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9733
Polymers21,8451
Non-polymers1272
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.720, 69.070, 119.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 21845.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: def, BMULJ_00106 / Plasmid: BumuA.00078.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KB98, peptide deformylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.98 Å3/Da / Density % sol: 37.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BumuA.00078.a.B1.PS37840 at 14mg/ml, mixed 1:1 with MCSG1(b5), 0.2M MgCl2, 0.1M Tris HCl pH 8.5, 25% (w/v) PEG 3350, cryo protected with 20% EG in 2 steps

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 12954 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 29.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.64
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.95-26.90.4973.561100
2-2.060.3814.69199.9
2.06-2.120.3175.89199.8
2.12-2.180.257.36199.9
2.18-2.250.1969.041100
2.25-2.330.17110.19199.5
2.33-2.420.14312.06199.7
2.42-2.520.12713.65199.4
2.52-2.630.10316.35199.9
2.63-2.760.08619.11199.1
2.76-2.910.07521.66199.6
2.91-3.080.06424.68199.1
3.08-3.30.0626.75199
3.3-3.560.05229.42198.9
3.56-3.90.04831.88199.4
3.9-4.360.04333.15199
4.36-5.030.0433.77199.3
5.03-6.170.04133.12198.6
6.17-8.720.03732.25198.3
8.720.03730.8195.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W3T

2w3t


Resolution: 1.95→29.923 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.01
RfactorNum. reflection% reflection
Rfree0.2068 1322 10.21 %
Rwork0.1735 --
obs0.1769 12944 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.47 Å2 / Biso mean: 40.0215 Å2 / Biso min: 20.19 Å2
Refinement stepCycle: final / Resolution: 1.95→29.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1321 0 5 85 1411
Biso mean--41.03 40.93 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071349
X-RAY DIFFRACTIONf_angle_d0.8411825
X-RAY DIFFRACTIONf_chiral_restr0.053210
X-RAY DIFFRACTIONf_plane_restr0.005238
X-RAY DIFFRACTIONf_dihedral_angle_d14.523838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.0280.26721470.222912781425100
2.028-2.12030.24041230.213212911414100
2.1203-2.23210.2621630.194712711434100
2.2321-2.37190.21991580.190312631421100
2.3719-2.55490.24931680.199312391407100
2.5549-2.81180.23661500.19131274142499
2.8118-3.21830.20451560.19471290144699
3.2183-4.05310.18451180.15591343146199
4.0531-29.92650.1651390.14471373151299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0193-1.4075-0.05783.30811.34134.85650.2072-0.5354-0.26540.5152-0.3490.05130.65810.37590.26820.3802-0.0043-0.02750.3341-0.00210.34124.535612.105324.9452
24.24750.45061.14843.95740.65274.2083-0.00350.3552-0.4669-0.17790.04570.14420.9637-0.0893-0.02810.4004-0.07660.02120.2324-0.04510.262717.49499.026615.4847
32.8259-0.3184-0.45056.2789-1.61980.7037-0.07390.86010.2131-1.33720.34610.32380.2947-0.3518-0.28520.526-0.1348-0.10680.58510.03480.283812.148417.46353.1053
44.5779-0.51222.88255.495-1.54284.9511-0.43620.19250.5944-0.0287-0.02320.5692-0.9918-0.5830.38330.3664-0.0158-0.06860.27580.01630.33716.006827.996816.5699
52.8972-0.43850.62435.1104-0.59380.55130.24970.1446-0.5652-0.29-0.26851.17730.6107-1.08890.07790.6418-0.2174-0.11360.6349-0.11270.45189.224410.33263.4445
61.5954-0.13081.6455.43262.54365.9428-0.26150.67870.0632-0.63390.01640.44790.1638-0.44390.28820.322-0.1286-0.04740.42290.01560.253712.744318.18998.6145
73.88270.94280.73696.5356-2.24461.0705-0.43250.71520.256-0.9540.2437-0.3571-1.06060.55250.07430.3939-0.1420.00360.37130.09220.249624.655327.007613.7826
82.95932.5593-3.66795.2948-4.26894.9115-0.2557-0.23490.155-0.1619-0.1219-0.4037-0.49280.76510.39150.3668-0.119-0.04370.2067-0.01240.346329.543727.745127.6915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 25 )A13 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 84 )A26 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 98 )A85 - 98
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 120 )A99 - 120
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 132 )A121 - 132
6X-RAY DIFFRACTION6chain 'A' and (resid 133 through 154 )A133 - 154
7X-RAY DIFFRACTION7chain 'A' and (resid 155 through 163 )A155 - 163
8X-RAY DIFFRACTION8chain 'A' and (resid 164 through 181 )A164 - 181

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