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- PDB-6lzt: N409A mutant of chitin-specific solute binding protein from Vibri... -

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Basic information

Entry
Database: PDB / ID: 6lzt
TitleN409A 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: 1.853 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 1.4Nov 13, 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)61,4924
Polymers61,0031
Non-polymers4893
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-17 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.466, 56.444, 80.881
Angle α, β, γ (deg.)90.00, 100.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 61002.758 Da / Num. of mol.: 1 / Mutation: N409A
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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 1.63mM chitobiose, 0.06 M Divalents (MgCl2, CaCl2), 0.1M Buffer System 1 (Imidazole, MES (acid)), pH 6.5, 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: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 44321 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.067 / Rrim(I) all: 0.131 / Rsym value: 0.131 / Net I/σ(I): 27
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.687 / Num. unique obs: 2194 / CC1/2: 0.817 / Rpim(I) all: 0.423 / Rrim(I) all: 0.809 / Rsym value: 1.393

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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: 1.853→23.647 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.38
RfactorNum. reflection% reflection
Rfree0.2958 2236 5.05 %
Rwork0.2355 --
obs0.2386 44261 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.853→23.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4243 0 31 135 4409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084448
X-RAY DIFFRACTIONf_angle_d1.1156065
X-RAY DIFFRACTIONf_dihedral_angle_d14.5791603
X-RAY DIFFRACTIONf_chiral_restr0.051645
X-RAY DIFFRACTIONf_plane_restr0.006795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8533-1.89350.3871170.31862139X-RAY DIFFRACTION82
1.8935-1.93760.33011450.30332640X-RAY DIFFRACTION100
1.9376-1.9860.34731380.29972634X-RAY DIFFRACTION100
1.986-2.03970.35791100.2872676X-RAY DIFFRACTION100
2.0397-2.09960.32381370.29132674X-RAY DIFFRACTION100
2.0996-2.16740.39911290.27592651X-RAY DIFFRACTION100
2.1674-2.24480.34081340.27012641X-RAY DIFFRACTION100
2.2448-2.33460.32691610.27812640X-RAY DIFFRACTION100
2.3346-2.44070.33161510.25532638X-RAY DIFFRACTION100
2.4407-2.56930.27851510.25422654X-RAY DIFFRACTION100
2.5693-2.730.30731460.2592656X-RAY DIFFRACTION100
2.73-2.94040.29791450.25832651X-RAY DIFFRACTION100
2.9404-3.23570.32961390.24192683X-RAY DIFFRACTION100
3.2357-3.70240.27571390.22282677X-RAY DIFFRACTION100
3.7024-4.65870.24451420.18692700X-RAY DIFFRACTION100
4.6587-23.60.27071520.20112671X-RAY DIFFRACTION97

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