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- PDB-6lzu: F411A mutant of chitin-specific solute binding protein from Vibri... -

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Basic information

Entry
Database: PDB / ID: 6lzu
TitleF411A mutant of chitin-specific solute binding protein from Vibrio harveyi co-crystalized with chitobiose.
ComponentsPeptide ABC transporter, periplasmic peptide-binding protein
KeywordsSUGAR BINDING PROTEIN / complex / chitin / periplasmic solute-binding protein / Vibrios
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle
Similarity search - Domain/homology
Peptide ABC transporter, periplasmic peptide-binding protein
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKitaoku, Y. / Ubonbal, P. / Tran, L.T. / Robinson, R.C. / Suginta, W.
Funding support Thailand, 2items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology300/111100/1711111000030 Thailand
Thailand Research FundBRG610008 Thailand
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A structural model for (GlcNAc) 2 translocation via a periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria.
Authors: Kitaoku, Y. / Fukamizo, T. / Kumsaoad, S. / Ubonbal, P. / Robinson, R.C. / Suginta, W.
History
DepositionFeb 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: 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: Peptide ABC transporter, periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7209
Polymers60,9701
Non-polymers7518
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.317, 57.231, 82.017
Angle α, β, γ (deg.)90.00, 100.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Peptide ABC transporter, periplasmic peptide-binding protein / Chitin-specific solute-binding protein


Mass: 60969.688 Da / Num. of mol.: 1 / Mutation: F411A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (strain 1DA3) (bacteria)
Gene: VME_26970 / Production host: Escherichia coli (E. coli) / References: UniProt: D0XC84
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 263 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 1.63mM chitobiose, 0.06M Divalents (MgCl2, CaCl2), 0.1M Buffer System 1 (Imidazole, MES (acid)), pH 6.5, 30% v/v Precipitant Mix 2 (Ethylene glycol, PEG 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 44296 / % possible obs: 98.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.068 / Rrim(I) all: 0.126 / Rsym value: 0.095 / Net I/σ(I): 10.76
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.105 / Num. unique obs: 2069 / CC1/2: 0.164 / Rpim(I) all: 0.068 / Rrim(I) all: 0.126 / Rsym value: 0.095

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5yqw

5yqw


Resolution: 1.9→24.15 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.63
RfactorNum. reflection% reflection
Rfree0.2336 2071 5.05 %
Rwork0.1858 --
obs0.1882 40989 90.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 45 256 4451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084319
X-RAY DIFFRACTIONf_angle_d1.0375894
X-RAY DIFFRACTIONf_dihedral_angle_d12.0521514
X-RAY DIFFRACTIONf_chiral_restr0.047634
X-RAY DIFFRACTIONf_plane_restr0.005775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94120.2792610.21071219X-RAY DIFFRACTION43
1.9412-1.98980.2677980.21241674X-RAY DIFFRACTION60
1.9898-2.04350.2911230.21562320X-RAY DIFFRACTION81
2.0435-2.10360.28231380.21352651X-RAY DIFFRACTION93
2.1036-2.17150.25321540.19832789X-RAY DIFFRACTION98
2.1715-2.24910.27811350.19722791X-RAY DIFFRACTION99
2.2491-2.3390.27081520.1932837X-RAY DIFFRACTION99
2.339-2.44540.23281500.19152834X-RAY DIFFRACTION100
2.4454-2.57420.2721400.19032859X-RAY DIFFRACTION99
2.5742-2.73530.24981300.2032875X-RAY DIFFRACTION99
2.7353-2.94610.21471520.18982830X-RAY DIFFRACTION99
2.9461-3.2420.26521730.19822819X-RAY DIFFRACTION99
3.242-3.70960.2271680.17692766X-RAY DIFFRACTION96
3.7096-4.66820.1851440.16072736X-RAY DIFFRACTION95
4.6682-24.14950.20021530.16962918X-RAY DIFFRACTION99

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