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- PDB-6onp: Crystal structure of periplasmic binding protein XoxJ from Methyl... -

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Basic information

Entry
Database: PDB / ID: 6onp
TitleCrystal structure of periplasmic binding protein XoxJ from Methylobacterium extorquens AM1
Componentsperiplasmic binding protein XoxJ
KeywordsUNKNOWN FUNCTION / perisplasmic binding protein / solute-binding protein / methanol dehydrogenase
Function / homologyQuinoprotein dehydrogenase-associated / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / PBPb domain-containing protein
Function and homology information
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å
AuthorsRose, H.R. / Taylor, E.M. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Chembiochem / Year: 2019
Title: Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide-Dependent Methanol Dehydrogenase Activity.
Authors: Featherston, E.R. / Rose, H.R. / McBride, M.J. / Taylor, E.M. / Boal, A.K. / Cotruvo Jr., J.A.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.3Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: periplasmic binding protein XoxJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2523
Polymers31,1281
Non-polymers1242
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.900, 51.759, 51.241
Angle α, β, γ (deg.)90.000, 98.237, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein periplasmic binding protein XoxJ


Mass: 31127.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: xoxJ, MexAM1_META1p1742 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5B122
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 9.0, 18% PEG 6000 / PH range: 8.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 12159 / % possible obs: 93.69 % / Redundancy: 5.4 % / Biso Wilson estimate: 29.35 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Net I/σ(I): 19.6
Reflection shellResolution: 2.27→2.3 Å / Rmerge(I) obs: 0.674 / Num. unique obs: 590 / CC1/2: 0.955 / Rpim(I) all: 0.304

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.27→49.39 Å / SU ML: 0.2384 / Cross valid method: FREE R-VALUE / Phase error: 30.8938
RfactorNum. reflection% reflection
Rfree0.279 549 4.81 %
Rwork0.2395 --
obs0.2414 11410 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.94 Å2
Refinement stepCycle: LAST / Resolution: 2.27→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 8 42 1713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211699
X-RAY DIFFRACTIONf_angle_d0.53242291
X-RAY DIFFRACTIONf_chiral_restr0.0425260
X-RAY DIFFRACTIONf_plane_restr0.0037289
X-RAY DIFFRACTIONf_dihedral_angle_d2.33931038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.490.33521040.28172147X-RAY DIFFRACTION74.81
2.49-2.850.33941370.2782881X-RAY DIFFRACTION99.83
2.85-3.60.31551620.25662880X-RAY DIFFRACTION100
3.6-49.40.22261460.20712953X-RAY DIFFRACTION99.9

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