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- PDB-6wpm: Crystal structure of a putative oligosaccharide periplasmic-bindi... -

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Basic information

Entry
Database: PDB / ID: 6wpm
TitleCrystal structure of a putative oligosaccharide periplasmic-binding protein from Synechococcus sp. MITs9220 in complex with zinc
ComponentsSubstrate-binding protein
KeywordsTRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / sugar-binding protein
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.88 Å
AuthorsFord, B.A. / Michie, K.A. / Paulsen, I.T. / Mabbutt, B.C. / Shah, B.S.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200102944 Australia
Australian Research Council (ARC)FL140100021 Australia
Citation
Journal: Sci Rep / Year: 2022
Title: Novel functional insights into a modified sugar-binding protein from Synechococcus MITS9220.
Authors: Ford, B.A. / Michie, K.A. / Paulsen, I.T. / Mabbutt, B.C. / Shah, B.S.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionApr 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,58715
Polymers47,3411
Non-polymers1,24614
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.778, 144.778, 53.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-503-

ZN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Substrate-binding protein


Mass: 47341.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: MITs9220 / Gene: 00121 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 5 types, 20 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Ammonium sulphate (2 M), PEG 3350 (20% w/v)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.23→53.42 Å / Num. obs: 13405 / % possible obs: 99.43 % / Redundancy: 3.8 % / Biso Wilson estimate: 86.28 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 0.0694
Reflection shellResolution: 2.88→2.98 Å / Redundancy: 2 % / Rmerge(I) obs: 0.027 / Mean I/σ(I) obs: 30 / Num. unique obs: 1253 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rrim(I) all: 0.038 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.15.2_3472refinement
pointlessdata reduction
SCALAdata scaling
PHASERphasing
Blu-Icedata collection
RefinementMethod to determine structure: SAD / Resolution: 2.88→45.78 Å / SU ML: 0.4011 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2539 664 4.95 %
Rwork0.2077 12741 -
obs0.2102 13405 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.88 Å2
Refinement stepCycle: LAST / Resolution: 2.88→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 62 6 3174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213222
X-RAY DIFFRACTIONf_angle_d0.49424404
X-RAY DIFFRACTIONf_chiral_restr0.036493
X-RAY DIFFRACTIONf_plane_restr0.0023573
X-RAY DIFFRACTIONf_dihedral_angle_d12.84961930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.10.37291300.29022431X-RAY DIFFRACTION97.27
3.1-3.410.31321080.25012535X-RAY DIFFRACTION100
3.41-3.910.26781290.21282523X-RAY DIFFRACTION100
3.91-4.920.22311340.18442564X-RAY DIFFRACTION99.96
4.92-45.780.24171630.19942688X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: 55.9373651946 Å / Origin y: 25.8361144798 Å / Origin z: 26.0606700515 Å
111213212223313233
T0.581259453824 Å20.0624221629646 Å20.00953049917604 Å2-0.58141718103 Å20.0197909190699 Å2--0.625297713117 Å2
L1.15161966474 °2-0.673742216907 °2-0.149097100299 °2-3.16382237482 °2-0.212084384883 °2--1.24887702884 °2
S-0.0518445668125 Å °-0.0507530458463 Å °-0.174081887744 Å °-0.0460033058483 Å °0.0578343028151 Å °0.274755526908 Å °0.288926533451 Å °0.182011915143 Å °-0.0146728169529 Å °
Refinement TLS groupSelection details: all

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