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- PDB-8x1a: Crystal structure of periplasmic G6P binding protein VcA0625 -

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Basic information

Entry
Database: PDB / ID: 8x1a
TitleCrystal structure of periplasmic G6P binding protein VcA0625
ComponentsIron(III) ABC transporter, periplasmic iron-compound-binding protein
KeywordsSUGAR BINDING PROTEIN / Vibrio cholerae / ABC transporter / periplasmic ligand binding protein
Function / homologyBacterial extracellular solute-binding protein / Ferric binding protein / 6-O-phosphono-alpha-D-glucopyranose / Iron(III) ABC transporter, periplasmic iron-compound-binding protein
Function and homology information
Biological speciesVibrio cholerae O395 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.604 Å
AuthorsDasgupta, J. / Saha, I.
Funding support India, 1items
OrganizationGrant numberCountry
Other private India
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural insights in to the atypical type-I ABC Glucose-6-phosphate importer VCA0625-27 of Vibrio cholerae.
Authors: Saha, I. / Ghosh, B. / Dasgupta, J.
History
DepositionNov 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: 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 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
B: Iron(III) ABC transporter, periplasmic iron-compound-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6742
Polymers35,4141
Non-polymers2601
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-4 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.288, 63.312, 75.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Iron(III) ABC transporter, periplasmic iron-compound-binding protein


Mass: 35413.684 Da / Num. of mol.: 1 / Mutation: A296T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: VC0395_0625 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3AFK0
#2: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.9 Å3/Da / Density % sol: 35.35 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: PEG 400, phosphate-citrate

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Data collection

DiffractionMean temperature: 294.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→45.6 Å / Num. obs: 36010 / % possible obs: 98.7 % / Redundancy: 4.6 % / CC1/2: 0.99 / Net I/σ(I): 19.8
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.344 / Num. unique obs: 1545

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.604→31.47 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1963 1774 4.94 %
Rwork0.1633 --
obs0.1649 35944 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.604→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 16 217 2701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122537
X-RAY DIFFRACTIONf_angle_d1.413433
X-RAY DIFFRACTIONf_dihedral_angle_d14.156933
X-RAY DIFFRACTIONf_chiral_restr0.088372
X-RAY DIFFRACTIONf_plane_restr0.007445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6043-1.64770.28381220.23632384X-RAY DIFFRACTION91
1.6477-1.69610.28421370.20472598X-RAY DIFFRACTION98
1.6961-1.75090.22921250.19482598X-RAY DIFFRACTION99
1.7509-1.81350.24761530.18052598X-RAY DIFFRACTION99
1.8135-1.88610.19881300.18142615X-RAY DIFFRACTION99
1.8861-1.97190.24211360.17552640X-RAY DIFFRACTION100
1.9719-2.07580.22341490.1692628X-RAY DIFFRACTION100
2.0758-2.20590.17481380.1622638X-RAY DIFFRACTION99
2.2059-2.37610.20561470.15342645X-RAY DIFFRACTION99
2.3761-2.61510.19491330.15362645X-RAY DIFFRACTION99
2.6151-2.99330.17821350.15852681X-RAY DIFFRACTION99
2.9933-3.77020.19361440.1472709X-RAY DIFFRACTION99
3.7702-31.46620.14191250.15332791X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.34940.17230.04081.5284-0.64331.08610.03020.0728-0.0905-0.1129-0.00620.01870.0953-0.0253-0.02130.10560.0017-0.00680.1061-0.01390.0976-10.735-14.80670.5441
22.49020.4854-0.15483.1836-1.93294.3675-0.0088-0.06380.22410.2310.11410.1175-0.2698-0.2441-0.07510.1010.03070.00570.1581-0.00470.1645-21.6032-2.71896.993
30.95920.54270.18921.24250.27920.4769-0.02090.00050.0457-0.02330.0077-0.0947-0.0690.0432-0.00250.10690.0066-0.00290.10150.00430.10435.58457.9676.5711
43.1478-1.92531.05791.9546-0.55590.6667-0.08770.25190.2315-0.0808-0.0579-0.1140.01060.03650.15090.1721-0.0242-0.00980.12670.00640.13786.457611.6638-2.659
52.4542.38952.37542.51021.84874.99740.0433-0.0078-0.2665-0.02720.1068-0.37780.15310.2611-0.1330.10530.01220.0110.1214-0.01470.159411.0837-2.93516.1802
60.95770.85220.37251.54820.16150.31780.0125-0.0057-0.0193-0.0167-0.0046-0.00020.0017-0.0009-0.0160.09560.00720.00480.1005-0.00660.0877-5.2613-5.11398.863
70.76810.5543-0.38540.9648-0.46311.44970.0427-0.05750.03490.0845-0.01220.0519-0.0624-0.0104-0.03310.12640.01060.00460.1204-0.00740.1304-9.7683-2.0814.9401
85.5293-0.44740.98593.7174-0.04763.3205-0.01610.0861-0.086-0.2437-0.0224-0.1598-0.03920.23030.0450.15870.00310.00550.13580.01570.1254-2.57427.7593-10.0074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid -2 through 78 )
2X-RAY DIFFRACTION2chain 'B' and (resid 79 through 99 )
3X-RAY DIFFRACTION3chain 'B' and (resid 100 through 162 )
4X-RAY DIFFRACTION4chain 'B' and (resid 163 through 181 )
5X-RAY DIFFRACTION5chain 'B' and (resid 182 through 197 )
6X-RAY DIFFRACTION6chain 'B' and (resid 198 through 251 )
7X-RAY DIFFRACTION7chain 'B' and (resid 252 through 299 )
8X-RAY DIFFRACTION8chain 'B' and (resid 300 through 316 )

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