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- PDB-1jvy: Maltodextrin-binding protein variant D207C/A301GS/P316C with beta... -

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Basic information

Entry
Database: PDB / ID: 1jvy
TitleMaltodextrin-binding protein variant D207C/A301GS/P316C with beta-mercaptoethanol mixed disulfides
Componentsmaltodextrin-binding protein
KeywordsTRANSPORT PROTEIN / intermolecular / cross-link / disulfide
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSrinivasan, U. / Iyer, G.H. / Przybycien, T.A. / Samsonoff, W.A. / Bell, J.A.
CitationJournal: Protein Eng. / Year: 2002
Title: Crystine: Fibrous Biomolecular Material from Protein Crystals Cross-linked in a Specific Geometry
Authors: Srinivasan, U. / Iyer, G.H. / Przybycien, T.A. / Samsonoff, W.A. / Bell, J.A.
History
DepositionAug 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4462
Polymers41,1041
Non-polymers3421
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.200, 68.100, 56.340
Angle α, β, γ (deg.)90.00, 112.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein maltodextrin-binding protein / MALTOSE-BINDING PERIPLASMIC PROTEIN


Mass: 41103.719 Da / Num. of mol.: 1 / Mutation: D207C/A301GS/P316C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE / Plasmid: pMAL-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2058 / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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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: 44.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 6000, sodium MES, maltose, sodium azide, beta-mercaptoethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5-10 mg/mlprotein1drop
29-15 %(w/v)PEG60001drop
310 mMMES-Na1drop
41 mMmaltose1drop
50.02 %sodium azide1drop
619-22 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å
DetectorType: BRANDEIS - B1 / Detector: CCD / Date: Jun 6, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→23.86 Å / Num. all: 28657 / Num. obs: 28657 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.9→2.5 Å / Mean I/σ(I) obs: 5.6 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 9999 Å / % possible obs: 100 % / Num. measured all: 127321 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNX2000.1refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MDQ

1mdq


Resolution: 1.9→23.86 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1416969.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2827 9.9 %RANDOM
Rwork0.207 ---
all0.25 28657 --
obs0.25 28520 100 %-
Solvent computationSolvent model: BABINET / Bsol: 280 Å2 / ksol: 0.9 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å2-4.11 Å2
2--1.18 Å20 Å2
3----3.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→23.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 23 371 3306
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it3.031.5
X-RAY DIFFRACTIONc_mcangle_it3.812
X-RAY DIFFRACTIONc_scbond_it4.432
X-RAY DIFFRACTIONc_scangle_it5.522.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 488 10.3 %
Rwork0.231 4257 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4CME.PARAMCME.TOP
Software
*PLUS
Name: CNX / Version: 2000.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07
X-RAY DIFFRACTIONc_mcbond_it3.031.5
X-RAY DIFFRACTIONc_scbond_it4.432
X-RAY DIFFRACTIONc_mcangle_it3.812
X-RAY DIFFRACTIONc_scangle_it5.522.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.303 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.231

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