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- PDB-6a55: Crystal structure of DddK mutant Y122A -

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Basic information

Entry
Database: PDB / ID: 6a55
TitleCrystal structure of DddK mutant Y122A
ComponentsNovel protein with potential Cupin domain
KeywordsLYASE / DMSP lyase
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / outer membrane-bounded periplasmic space / metal ion binding / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid / : / Novel protein with potential Cupin domain
Function and homology information
Biological speciesPelagibacter ubique (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, Y.Z. / Li, C.Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (China)31728001 China
National Science Foundation (China)31630012 China
National Science Foundation (China)41706152 China
CitationJournal: Appl. Environ. Microbiol. / Year: 2019
Title: Structure-Function Analysis Indicates that an Active-Site Water Molecule Participates in Dimethylsulfoniopropionate Cleavage by DddK.
Authors: Peng, M. / Chen, X.L. / Zhang, D. / Wang, X.J. / Wang, N. / Wang, P. / Todd, J.D. / Zhang, Y.Z. / Li, C.Y.
History
DepositionJun 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Novel protein with potential Cupin domain
B: Novel protein with potential Cupin domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7366
Polymers30,3542
Non-polymers3824
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-26 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.802, 49.101, 76.226
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Novel protein with potential Cupin domain


Mass: 15177.058 Da / Num. of mol.: 2 / Mutation: Y122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelagibacter ubique (strain HTCC1062) (bacteria)
Strain: HTCC1062 / Gene: SAR11_0394 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4FNM4
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-DQY / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid


Mass: 136.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M Hepes (pH 7.5) and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 35370 / % possible obs: 98.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 37.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6 % / Rmerge(I) obs: 0.3 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A53

6a53


Resolution: 1.6→35.135 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.59
RfactorNum. reflection% reflection
Rfree0.2179 1707 4.94 %
Rwork0.1618 --
obs0.1646 34540 95.91 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 40.154 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.7084 Å20 Å23.056 Å2
2--0.8384 Å2-0 Å2
3----12.5468 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 18 285 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052039
X-RAY DIFFRACTIONf_angle_d0.942765
X-RAY DIFFRACTIONf_dihedral_angle_d13.613725
X-RAY DIFFRACTIONf_chiral_restr0.066298
X-RAY DIFFRACTIONf_plane_restr0.003351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5924-1.63930.2571150.17642276X-RAY DIFFRACTION80
1.6393-1.69220.25241430.15962582X-RAY DIFFRACTION92
1.6922-1.75270.22091460.15342701X-RAY DIFFRACTION94
1.7527-1.82280.21451500.14172680X-RAY DIFFRACTION96
1.8228-1.90580.2091390.13492724X-RAY DIFFRACTION96
1.9058-2.00620.22831360.14442794X-RAY DIFFRACTION97
2.0062-2.13190.24461810.162766X-RAY DIFFRACTION99
2.1319-2.29650.23491390.15382789X-RAY DIFFRACTION98
2.2965-2.52760.2371230.16142834X-RAY DIFFRACTION99
2.5276-2.89320.22291470.17472872X-RAY DIFFRACTION100
2.8932-3.64450.21971270.16542896X-RAY DIFFRACTION100
3.6445-35.14380.19351610.16592919X-RAY DIFFRACTION100

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