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- PDB-6lzq: Chitin-specific solute binding protein from Vibrio harveyi in com... -

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Basic information

Entry
Database: PDB / ID: 6lzq
TitleChitin-specific solute binding protein from Vibrio harveyi in complex with chitotriose.
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
triacetyl-beta-chitotriose / Peptide ABC transporter, periplasmic peptide-binding protein
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 30, 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)62,67218
Polymers61,2881
Non-polymers1,38417
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-16 kcal/mol
Surface area20920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.833, 56.838, 81.864
Angle α, β, γ (deg.)90.00, 99.40, 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)
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-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 353 molecules

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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 1.63mM chitotriose, 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: 1.8→50 Å / Num. obs: 48470 / % possible obs: 92.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.085 / Rrim(I) all: 0.155 / Rsym value: 0.155 / Net I/σ(I): 8.79
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 1.114 / Num. unique obs: 2253 / CC1/2: 0.262 / Rpim(I) all: 0.765 / Rrim(I) all: 1.362 / Rsym value: 1.656

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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: 1.8→36.531 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 2123 4.9 %
Rwork0.1641 --
obs0.1662 43328 83.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→36.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4295 0 83 337 4715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074543
X-RAY DIFFRACTIONf_angle_d1.0526182
X-RAY DIFFRACTIONf_dihedral_angle_d13.1541647
X-RAY DIFFRACTIONf_chiral_restr0.046667
X-RAY DIFFRACTIONf_plane_restr0.006801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84190.2723990.1891894X-RAY DIFFRACTION58
1.8419-1.88790.23951100.18122149X-RAY DIFFRACTION66
1.8879-1.9390.251120.17372365X-RAY DIFFRACTION72
1.939-1.9960.21681440.16892498X-RAY DIFFRACTION76
1.996-2.06040.22231290.17162607X-RAY DIFFRACTION79
2.0604-2.13410.19551480.16762707X-RAY DIFFRACTION83
2.1341-2.21950.24851440.17122793X-RAY DIFFRACTION85
2.2195-2.32050.21331180.17562812X-RAY DIFFRACTION85
2.3205-2.44280.23131630.18022875X-RAY DIFFRACTION87
2.4428-2.59580.24491430.18332951X-RAY DIFFRACTION89
2.5958-2.79620.20831530.17213143X-RAY DIFFRACTION95
2.7962-3.07750.21811830.17613267X-RAY DIFFRACTION99
3.0775-3.52250.18871760.15923308X-RAY DIFFRACTION100
3.5225-4.43670.19971390.13952653X-RAY DIFFRACTION79
4.4367-36.50.16571620.15283183X-RAY DIFFRACTION93

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