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- PDB-7ebi: Chitin-specific solute binding protein from Vibrio harveyi co-cry... -

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Basic information

Entry
Database: PDB / ID: 7ebi
TitleChitin-specific solute binding protein from Vibrio harveyi co-crystalized with chitotetraose.
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: 1.5 Å
AuthorsKitaoku, Y. / Ubonbal, P. / Tran, L.T. / Robinson, R.C. / Suginta, W.
Funding support Thailand, 2items
OrganizationGrant numberCountry
Other privateVidyasirimedhi Institute of Science and Technology, 300/111100/1711111000030 Thailand
Other governmentThailand Research Fund, BRG610008 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
DepositionMar 9, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 8, 2021ID: 6LZR
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Mar 12, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details / 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)62,76823
Polymers61,2881
Non-polymers1,48022
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.877, 57.107, 82.134
Angle α, β, γ (deg.)90.00, 99.54, 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: 61288.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (strain 1DA3) (bacteria)
Strain: 1DA3 / 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: obtained synthetically
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, 329 molecules

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


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 1.63mM chitotetramer, 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: 1.5→50 Å / Num. obs: 89117 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.076 / Net I/σ(I): 19.99
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.3 % / Num. unique obs: 4293 / CC1/2: 0.762 / Rpim(I) all: 0.312 / Rrim(I) all: 0.506 / % possible all: 95.7

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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: 1.5→24.49 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 4261 4.89 %
Rwork0.1736 --
obs0.1745 87087 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4293 0 89 308 4690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064539
X-RAY DIFFRACTIONf_angle_d1.0676170
X-RAY DIFFRACTIONf_dihedral_angle_d12.0081633
X-RAY DIFFRACTIONf_chiral_restr0.046655
X-RAY DIFFRACTIONf_plane_restr0.006807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51330.26581150.22432247X-RAY DIFFRACTION78
1.5133-1.53110.2541080.21232477X-RAY DIFFRACTION86
1.5311-1.54980.24751300.20862578X-RAY DIFFRACTION89
1.5498-1.56940.25031390.20132588X-RAY DIFFRACTION91
1.5694-1.590.22491370.18612715X-RAY DIFFRACTION93
1.59-1.61180.21641660.18852678X-RAY DIFFRACTION94
1.6118-1.63480.22191520.1752730X-RAY DIFFRACTION96
1.6348-1.65920.20121310.18062780X-RAY DIFFRACTION96
1.6592-1.68510.21681580.17572839X-RAY DIFFRACTION98
1.6851-1.71280.21041300.17622808X-RAY DIFFRACTION98
1.7128-1.74230.19711390.16942846X-RAY DIFFRACTION99
1.7423-1.7740.19931690.17342846X-RAY DIFFRACTION99
1.774-1.80810.1991390.17342870X-RAY DIFFRACTION99
1.8081-1.8450.19781680.17422850X-RAY DIFFRACTION100
1.845-1.88510.22981430.16652874X-RAY DIFFRACTION100
1.8851-1.92890.19541470.1682867X-RAY DIFFRACTION100
1.9289-1.97710.18761510.16142899X-RAY DIFFRACTION100
1.9771-2.03060.17041460.16192870X-RAY DIFFRACTION100
2.0306-2.09030.2151630.16962884X-RAY DIFFRACTION100
2.0903-2.15770.2091460.1672882X-RAY DIFFRACTION100
2.1577-2.23480.19131540.17392875X-RAY DIFFRACTION100
2.2348-2.32420.20781480.17872858X-RAY DIFFRACTION100
2.3242-2.42990.19451380.17832914X-RAY DIFFRACTION100
2.4299-2.55790.19971490.17422906X-RAY DIFFRACTION99
2.5579-2.71790.1921180.17952899X-RAY DIFFRACTION99
2.7179-2.92750.16381500.17652834X-RAY DIFFRACTION99
2.9275-3.22150.21011290.18232897X-RAY DIFFRACTION99
3.2215-3.68630.18751220.16662741X-RAY DIFFRACTION98
3.6863-4.63910.12171240.15132034X-RAY DIFFRACTION75
4.6391-24.490.18671520.17622740X-RAY DIFFRACTION92

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