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- PDB-5wjp: Crystal structure of the cyclohexadienyl dehydratase-like solute-... -

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Basic information

Entry
Database: PDB / ID: 5wjp
TitleCrystal structure of the cyclohexadienyl dehydratase-like solute-binding protein SAR11_1068 from Candidatus Pelagibacter ubique.
ComponentsCyclohexadienyl dehydratase
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute-binding protein
Function / homology
Function and homology information


Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cyclohexadienyl dehydratase
Similarity search - Component
Biological speciesPelagibacter ubique (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsClifton, B.E. / Jackson, C.J.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.
Authors: Clifton, B.E. / Kaczmarski, J.A. / Carr, P.D. / Gerth, M.L. / Tokuriki, N. / Jackson, C.J.
History
DepositionJul 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclohexadienyl dehydratase


Theoretical massNumber of molelcules
Total (without water)27,8991
Polymers27,8991
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.730, 65.870, 90.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cyclohexadienyl dehydratase


Mass: 27898.885 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelagibacter ubique (bacteria) / Strain: HTCC1062 / Gene: pheC, SAR11_1068 / Plasmid: pDOTS7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4FLR5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.5 uL 18 mg/mL protein (10 mM TRIS pH 8.0, 100 mM NaCl, 10% glycerol) + 1.5 uL 24% PEG 8000, 5% PEG 400, 0.1 M BIS-TRIS propane pH 9.0.
PH range: 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2015
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.57→37.43 Å / Num. obs: 32445 / % possible obs: 97.3 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 12.7
Reflection shellResolution: 1.57→1.59 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.678 / Mean I/σ(I) obs: 1.9 / % possible all: 96.6

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Processing

Software
NameVersionClassification
MOSFLM7.0.9data reduction
Aimless0.1.29data scaling
PHASER2.5.2phasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KBR

3kbr


Resolution: 1.57→37.43 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.477 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1642 5.1 %RANDOM
Rwork0.183 ---
obs0.184 30761 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.57→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 0 207 2060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021929
X-RAY DIFFRACTIONr_bond_other_d0.0010.021880
X-RAY DIFFRACTIONr_angle_refined_deg2.1111.9722619
X-RAY DIFFRACTIONr_angle_other_deg0.90934369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04125.81174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73215365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.178154
X-RAY DIFFRACTIONr_chiral_restr0.1270.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
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_it1.6771.321961
X-RAY DIFFRACTIONr_mcbond_other1.6721.32960
X-RAY DIFFRACTIONr_mcangle_it2.4681.9811203
X-RAY DIFFRACTIONr_mcangle_other2.4691.9821204
X-RAY DIFFRACTIONr_scbond_it2.521.583968
X-RAY DIFFRACTIONr_scbond_other2.5151.583968
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7422.2571409
X-RAY DIFFRACTIONr_long_range_B_refined5.25311.4892411
X-RAY DIFFRACTIONr_long_range_B_other5.13211.1322326
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 128 -
Rwork0.351 2198 -
obs--95.41 %

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