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- PDB-3pgf: Crystal structure of maltose bound MBP with a conformationally sp... -

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Basic information

Entry
Database: PDB / ID: 3pgf
TitleCrystal structure of maltose bound MBP with a conformationally specific synthetic antigen binder (sAB)
Components
  • Maltose-binding periplasmic protein
  • SAB Heavy Chain
  • SAB Light Chain
KeywordsMALTODEXTRIN BINDING PROTEIN/DE NOVO PROTEIN / Maltodextrin binding protein / FAB / antibody fragment / engineered binding protein / MALTODEXTRIN BINDING PROTEIN-DE NOVO PROTEIN complex
Function / homology
Function and homology information


immunoglobulin complex / 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 ...immunoglobulin complex / 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 / adaptive immune response / periplasmic space / DNA damage response / extracellular region / metal ion binding / membrane / plasma 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 / Immunoglobulin V-Type / Periplasmic binding protein-like II / Immunoglobulin V-set domain ...: / 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 / Immunoglobulin V-Type / Periplasmic binding protein-like II / Immunoglobulin V-set domain / D-Maltodextrin-Binding Protein; domain 2 / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / IMIDAZOLE / Maltose/maltodextrin-binding periplasmic protein / Immunoglobulin gamma-1 heavy chain / Ig-like domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKossiakoff, A.A. / Duguid, E.M. / Sandstrom, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins.
Authors: Rizk, S.S. / Paduch, M. / Heithaus, J.H. / Duguid, E.M. / Sandstrom, A. / Kossiakoff, A.A.
History
DepositionNov 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein
H: SAB Heavy Chain
L: SAB Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8418
Polymers92,1763
Non-polymers6655
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-27 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.870, 228.460, 135.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11H-230-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody SAB Heavy Chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 24669.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686P15220, ighg / Plasmid: pfab007 / Production host: Escherichia coli (E. coli) / Strain (production host): actt 55244 (derived from w3110) / References: UniProt: P0DOX5
#3: Antibody SAB Light Chain


Mass: 23330.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: igk, IGK@ / Plasmid: pfab007 / Production host: Escherichia coli (E. coli) / Strain (production host): actt 55244 (derived from w3110) / References: UniProt: Q8TCD0

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 44175.613 Da / Num. of mol.: 1 / Mutation: r367n delta (368-370)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malE, b4034, JW3994 / Plasmid: phft2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEX9
#4: 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

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Non-polymers , 3 types, 404 molecules

#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SAB HEAVY AND LIGHT CHAINS CONTAIN BOTH A VARIABLE DOMAIN REPRESENTED BY THE SEQUENCE SELF ...THE SAB HEAVY AND LIGHT CHAINS CONTAIN BOTH A VARIABLE DOMAIN REPRESENTED BY THE SEQUENCE SELF REFERENCE AND A CONSTANT DOMAIN THAT REFERENCES THE UNIPROT DATABASE

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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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 19% PEG 3400, 8% Tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07817 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07817 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. all: 78510 / Num. obs: 74893 / % possible obs: 85.2 % / Observed criterion σ(F): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.83-1.862.30.51639.7
1.86-1.92.90.55152.1
1.9-1.933.40.5259.7
1.93-1.973.90.4365.1
1.97-2.014.20.36169
2.01-2.064.30.30372.9
2.06-2.114.40.27178.1
2.11-2.174.40.21984.1
2.17-2.234.40.19989.8
2.23-2.314.50.17795.2
2.31-2.394.60.16198.6
2.39-2.484.80.139100
2.48-2.650.117100
2.6-2.7350.088100
2.73-2.950.07399.9
2.9-3.1350.057100
3.13-3.444.90.05599.7
3.44-3.944.90.04399.6
3.94-4.974.90.03299.4
4.97-504.70.02998.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.6 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.68 Å
Translation2.5 Å39.68 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ANF and 2R8S

1anf

2r8s


Resolution: 2.1→38.07 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.785 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1912 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22664 2815 5 %RANDOM
Rwork0.17659 ---
obs0.17903 53794 97.04 %-
all-56609 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.964 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2--0.45 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6075 0 45 400 6520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0226366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.9638687
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.8955824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90925.08250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.985151039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4591517
X-RAY DIFFRACTIONr_chiral_restr0.140.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214785
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8421.54006
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38626481
X-RAY DIFFRACTIONr_scbond_it2.48932356
X-RAY DIFFRACTIONr_scangle_it3.6644.52181
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 194 -
Rwork0.214 3333 -
obs--82.79 %
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)
13.1124-0.7432-0.0092.97390.44473.0701-0.02090.1023-0.1358-0.3866-0.10730.40280.008-0.38410.12830.1512-0.0475-0.03620.0786-0.02270.1499-18.2159.881-15.918
20.4297-0.1527-0.09682.00541.171.9305-0.03570.003-0.0363-0.2027-0.00230.0736-0.081-0.03020.0380.0501-0.0160.00410.01230.00070.0325-8.43222.07-2.591
31.2270.0757-0.50122.21670.43042.5591-0.0365-0.0404-0.0871-0.08610.0286-0.16640.08190.13820.00790.0205-0.01290.02740.0303-0.02350.0442-2.55119.0512.277
44.06491.5132-2.54211.4036-1.30544.7833-0.0815-0.6327-0.0861-0.02270.018-0.25950.23290.42780.06350.3320.01770.22610.2031-0.01590.338829.34830.041-16.439
52.88850.5796-1.54690.6136-0.22181.211-0.11970.0037-0.0654-0.26020.064-0.27690.20270.0770.05580.2922-0.05010.19440.0534-0.04160.166618.21929.933-17.368
61.9044-0.145-0.31843.64621.70942.1828-0.232-0.1603-0.0931-0.05460.0132-0.23420.00160.13560.21880.11430.02420.06380.10480.04380.122840.88156.217-12.979
74.506611.23743.844645.85459.33583.9574-0.39140.1226-0.45470.56370.6068-2.369-0.0350.5883-0.21540.3320.22010.0530.41750.03910.392849.37855.112-9.525
81.49790.6061-0.70275.6061-0.41880.8303-0.18460.17410.1389-0.63780.13390.13230.0966-0.11410.05080.1464-0.08310.00950.0859-0.01240.06597.52947.699-17.917
93.6749-0.4022-1.27131.47320.07231.4631-0.0713-0.0021-0.0614-0.0509-0.0337-0.22210.04420.17180.10510.0931-0.01410.01770.05170.00840.046637.98466.211-23.911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 49
2X-RAY DIFFRACTION2A50 - 306
3X-RAY DIFFRACTION3A307 - 367
4X-RAY DIFFRACTION4H2 - 22
5X-RAY DIFFRACTION5H23 - 114
6X-RAY DIFFRACTION6H115 - 202
7X-RAY DIFFRACTION7H203 - 216
8X-RAY DIFFRACTION8L1 - 106
9X-RAY DIFFRACTION9L107 - 214

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