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- PDB-8ikr: Crystal structure of DpaA -

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Basic information

Entry
Database: PDB / ID: 8ikr
TitleCrystal structure of DpaA
ComponentsYkuD domain-containing protein
KeywordsHYDROLASE / peptidoglycan / amidase / YukD
Function / homologyL,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / peptidoglycan L,D-transpeptidase activity / peptidoglycan biosynthetic process / transferase activity / YkuD domain-containing protein
Function and homology information
Biological speciesEscherichia coli 908519 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, H.-J. / Hsieh, K.-Y. / Lee, S.-H. / Chang, C.-I.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)NSTC108-2320-B-001-011-MY3 Taiwan
CitationJournal: Mbio / Year: 2023
Title: Structural basis for the hydrolytic activity of the transpeptidase-like protein DpaA to detach Braun's lipoprotein from peptidoglycan.
Authors: Wang, H.J. / Hernandez-Rocamora, V.M. / Kuo, C.I. / Hsieh, K.Y. / Lee, S.H. / Ho, M.R. / Tu, Z. / Vollmer, W. / Chang, C.I.
History
DepositionMar 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YkuD domain-containing protein
B: YkuD domain-containing protein


Theoretical massNumber of molelcules
Total (without water)54,3382
Polymers54,3382
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-11 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.876, 86.876, 150.675
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein YkuD domain-containing protein


Mass: 27168.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 908519 (bacteria) / Gene: HMPREF1604_05013 / Production host: Escherichia coli (E. coli) / References: UniProt: V0UTF7

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 19-25% (w/v) PEG 3350, 0.1M Bis-Tris-HCl, pH 6-7, 0.2M ammonium acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→28.47 Å / Num. obs: 13361 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 0.999 / Rpim(I) all: 0.019 / Net I/σ(I): 26.07
Reflection shellResolution: 2.9→3.004 Å / Rmerge(I) obs: 0.2015 / Num. unique obs: 1280 / CC1/2: 0.982

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→28.47 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 55.802 / SU ML: 0.427 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 661 4.9 %RANDOM
Rwork0.21461 ---
obs0.21747 12702 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 111.576 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0 Å2
2--0.09 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.9→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 0 0 3033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123106
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162904
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.6634169
X-RAY DIFFRACTIONr_angle_other_deg0.7851.5786693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.55360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.439518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.11310542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023598
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02774
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_it2.93611.0141473
X-RAY DIFFRACTIONr_mcbond_other2.93611.0151473
X-RAY DIFFRACTIONr_mcangle_it4.75219.7021822
X-RAY DIFFRACTIONr_mcangle_other4.75119.7071823
X-RAY DIFFRACTIONr_scbond_it3.10511.5071633
X-RAY DIFFRACTIONr_scbond_other3.10411.5121634
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.86721.0292348
X-RAY DIFFRACTIONr_long_range_B_refined7.394110.393503
X-RAY DIFFRACTIONr_long_range_B_other7.394110.393503
X-RAY DIFFRACTIONr_rigid_bond_restr1.71736010
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 50 -
Rwork0.364 861 -
obs--98.17 %
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)
14.86560.63071.31343.22712.56327.3448-0.0645-0.05750.04070.07510.03160.478-0.43160.37560.03290.3844-0.02410.15230.3906-0.0230.50120.1524-0.892220.1428
226.7035-45.5269-31.526177.803753.832837.29130.29280.5562-0.2060.003-0.79680.451-0.0188-0.63690.5041.2575-0.25420.37890.84490.29080.93918.2438-13.428533.7329
34.93810.20182.22672.79930.88246.2792-0.01830.22530.0951-0.0685-0.00430.6813-0.49370.17230.02260.3215-0.01850.15810.2914-0.0320.564515.9837-2.606915.7058
41.4489-0.63690.49423.09371.58132.32490.3347-0.85490.31271.1218-0.56440.41060.181-0.66870.22971.5653-0.30220.50711.6194-0.20650.544421.06145.165252.506
53.38041.78511.69323.78712.81263.8530.3948-1.51480.49290.951-0.81390.559-0.0463-0.76750.41911.2489-0.19110.44581.3501-0.32910.457918.74669.199648.8716
64.01690.62460.81620.15690.28080.56660.1801-0.98760.16890.4032-0.37320.07251.0299-0.74910.19312.8095-0.71480.58212.6426-0.28620.571516.62663.475567.7814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 102
2X-RAY DIFFRACTION2A103 - 108
3X-RAY DIFFRACTION3A109 - 229
4X-RAY DIFFRACTION4B36 - 109
5X-RAY DIFFRACTION5B110 - 173
6X-RAY DIFFRACTION6B174 - 224

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