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- PDB-7ebm: W363A mutant of Chitin-specific solute binding protein from Vibri... -

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Basic information

Entry
Database: PDB / ID: 7ebm
TitleW363A mutant of Chitin-specific solute binding protein from Vibrio harveyi in complex 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
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 10, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 8, 2021ID: 6LZS
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 1.3Nov 20, 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)61,7997
Polymers61,1731
Non-polymers6266
Water4,702261
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 area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.574, 55.986, 80.319
Angle α, β, γ (deg.)90.00, 101.84, 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: 61172.926 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: 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, 266 molecules

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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 1.63mM chitobiose, 0.06M Divalents (MgCl2, CaCl2), 0.1M Buffer System 2 (Sodium HEPES, MOPS (acid)), pH 7.5, 50% v/v Precipitant Mix 4 (MPD, PEG 1000, PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97913 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 40844 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rpim(I) all: 0.075 / Rrim(I) all: 0.199 / Net I/σ(I): 401.1
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 2018 / CC1/2: 0.572 / Rpim(I) all: 0.796 / Rrim(I) all: 2.03

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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→23.732 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 1914 4.94 %
Rwork0.1833 --
obs0.1865 38780 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→23.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4235 0 37 261 4533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084408
X-RAY DIFFRACTIONf_angle_d1.0736008
X-RAY DIFFRACTIONf_dihedral_angle_d13.1911581
X-RAY DIFFRACTIONf_chiral_restr0.048640
X-RAY DIFFRACTIONf_plane_restr0.006790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93410.318830.27141501X-RAY DIFFRACTION54
1.9341-1.98640.3371040.26162145X-RAY DIFFRACTION78
1.9864-2.04480.30451460.24152513X-RAY DIFFRACTION91
2.0448-2.11080.34091330.22662706X-RAY DIFFRACTION97
2.1108-2.18620.29651500.21632765X-RAY DIFFRACTION99
2.1862-2.27360.28481520.21432750X-RAY DIFFRACTION100
2.2736-2.3770.29221240.20992802X-RAY DIFFRACTION100
2.377-2.50220.28881280.20012821X-RAY DIFFRACTION100
2.5022-2.65880.24571430.1992801X-RAY DIFFRACTION100
2.6588-2.86380.32351380.18752781X-RAY DIFFRACTION100
2.8638-3.15140.24491460.18422794X-RAY DIFFRACTION100
3.1514-3.6060.21921550.16542801X-RAY DIFFRACTION100
3.606-4.5380.19541450.14062834X-RAY DIFFRACTION100
4.538-23.730.19171670.14952852X-RAY DIFFRACTION99

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