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- PDB-7jtr: Complex of maltose-binding protein (MBP) with single-chain Fv (scFv) -

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Basic information

Entry
Database: PDB / ID: 7jtr
TitleComplex of maltose-binding protein (MBP) with single-chain Fv (scFv)
Components
  • Maltose/maltodextrin-binding periplasmic protein
  • single-chain Fv antibody fragment (scFv)
KeywordsSUGAR BINDING PROTEIN/IMMUNE SYSTEM / Maltose / antibody / scFv / complex / SUGAR BINDING PROTEIN / SUGAR BINDING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLoll, P.J.
CitationJournal: Protein Sci. / Year: 2021
Title: A useful epitope tag derived from maltose binding protein.
Authors: Lenon, M. / Ke, N. / Ren, G. / Meuser, M.E. / Loll, P.J. / Riggs, P. / Berkmen, M.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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: Maltose/maltodextrin-binding periplasmic protein
B: single-chain Fv antibody fragment (scFv)
C: Maltose/maltodextrin-binding periplasmic protein
D: single-chain Fv antibody fragment (scFv)
E: Maltose/maltodextrin-binding periplasmic protein
F: single-chain Fv antibody fragment (scFv)
G: Maltose/maltodextrin-binding periplasmic protein
H: single-chain Fv antibody fragment (scFv)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,44815
Polymers270,9728
Non-polymers1,4767
Water32418
1
A: Maltose/maltodextrin-binding periplasmic protein
B: single-chain Fv antibody fragment (scFv)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1214
Polymers67,7432
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Maltose/maltodextrin-binding periplasmic protein
D: single-chain Fv antibody fragment (scFv)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0853
Polymers67,7432
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Maltose/maltodextrin-binding periplasmic protein
F: single-chain Fv antibody fragment (scFv)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1214
Polymers67,7432
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Maltose/maltodextrin-binding periplasmic protein
H: single-chain Fv antibody fragment (scFv)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1214
Polymers67,7432
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.200, 91.700, 174.630
Angle α, β, γ (deg.)90.000, 91.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
41chain G
12(chain B and (resid 1 through 113 or resid 130 through 161 or resid 165 through 242))
22(chain D and (resid 1 through 161 or resid 165 through 242))
32(chain F and resid 1 through 242)
42(chain H and resid 1 through 242)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 369
211chain CC1 - 369
311chain EE1 - 369
411chain GG1 - 369
112(chain B and (resid 1 through 113 or resid 130 through 161 or resid 165 through 242))B1 - 113
122(chain B and (resid 1 through 113 or resid 130 through 161 or resid 165 through 242))B130 - 161
132(chain B and (resid 1 through 113 or resid 130 through 161 or resid 165 through 242))B165 - 242
212(chain D and (resid 1 through 161 or resid 165 through 242))D1 - 161
222(chain D and (resid 1 through 161 or resid 165 through 242))D165 - 242
312(chain F and resid 1 through 242)F1 - 242
412(chain H and resid 1 through 242)H1 - 242

NCS ensembles :
ID
1
2

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Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 40652.023 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Antibody
single-chain Fv antibody fragment (scFv)


Mass: 27091.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4 / Source method: isolated from a natural 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.81 Å3/Da / Density % sol: 56.26 % / Description: rods
Crystal growTemperature: 277 K / Method: microbatch / pH: 7.5 / Details: 0.2 M ammonium sulfate, 20% v/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→19.995 Å / Num. obs: 102294 / % possible obs: 98 % / Redundancy: 7.7 % / Biso Wilson estimate: 56.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.032 / Rrim(I) all: 0.091 / Net I/σ(I): 14.85
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 9974 / CC1/2: 0.888 / Rpim(I) all: 0.354 / Rrim(I) all: 1.01 / % possible all: 96.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDS20161205data reduction
XSCALE20161205data scaling
PHASERv2.7.16phasing
PHENIXv1.11.1refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF,2GKI

1anf

2gki


Resolution: 2.5→19.995 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / Phase error: 33.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1979 1.94 %random
Rwork0.2005 100183 --
obs0.2012 102162 98.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.98 Å2 / Biso mean: 66.8237 Å2 / Biso min: 37.33 Å2
Refinement stepCycle: final / Resolution: 2.5→19.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18401 0 95 18 18514
Biso mean--60.81 52.31 -
Num. residues----2372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118947
X-RAY DIFFRACTIONf_angle_d1.50525722
X-RAY DIFFRACTIONf_chiral_restr0.0812829
X-RAY DIFFRACTIONf_plane_restr0.0083294
X-RAY DIFFRACTIONf_dihedral_angle_d9.65111236
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7028X-RAY DIFFRACTION13.564TORSIONAL
12C7028X-RAY DIFFRACTION13.564TORSIONAL
13E7028X-RAY DIFFRACTION13.564TORSIONAL
14G7028X-RAY DIFFRACTION13.564TORSIONAL
21B4124X-RAY DIFFRACTION13.564TORSIONAL
22D4124X-RAY DIFFRACTION13.564TORSIONAL
23F4124X-RAY DIFFRACTION13.564TORSIONAL
24H4124X-RAY DIFFRACTION13.564TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.56250.38191310.3316693996
2.5625-2.63160.35431500.3139707298
2.6316-2.70880.38611350.3022712998
2.7088-2.79610.37891340.2914711498
2.7961-2.89570.31711420.2696712198
2.8957-3.01130.35151330.2656715698
3.0113-3.14780.32661530.2521716999
3.1478-3.31310.30761270.2469712998
3.3131-3.51960.29831540.2262720499
3.5196-3.78970.23741420.2082720099
3.7897-4.16790.21231480.1816721499
4.1679-4.76390.19841350.151711497
4.7639-5.97530.17231440.1622730099
5.9753-19.9950.16391510.1552732298

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