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- PDB-5bk1: Crystal structure of maltose binding protein in complex with an e... -

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Basic information

Entry
Database: PDB / ID: 5bk1
TitleCrystal structure of maltose binding protein in complex with an endosteric synthetic antibody
Components
  • (Synthetic antibody, Fab fragment, ...) x 2
  • Maltose binding proteinMaltose-binding protein
KeywordsSUGAR BINDING PROTEIN / Maltose binding protein / conformation specific synthetic antibody
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMukherjee, S. / Kossiakoff, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Chicago Biomedical Consortium United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Engineered synthetic antibodies as probes to quantify the energetic contributions of ligand binding to conformational changes in proteins.
Authors: Mukherjee, S. / Griffin, D.H. / Horn, J.R. / Rizk, S.S. / Nocula-Lugowska, M. / Malmqvist, M. / Kim, S.S. / Kossiakoff, A.A.
History
DepositionSep 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Synthetic antibody, Fab fragment, Heavy Chain
L: Synthetic antibody, Fab fragment, Light Chain
C: Synthetic antibody, Fab fragment, Heavy Chain
D: Synthetic antibody, Fab fragment, Light Chain
A: Maltose binding protein
B: Maltose binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,5949
Polymers185,3756
Non-polymers2203
Water17,727984
1
H: Synthetic antibody, Fab fragment, Heavy Chain
L: Synthetic antibody, Fab fragment, Light Chain
A: Maltose binding protein


Theoretical massNumber of molelcules
Total (without water)92,6873
Polymers92,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-35 kcal/mol
Surface area33540 Å2
MethodPISA
2
C: Synthetic antibody, Fab fragment, Heavy Chain
D: Synthetic antibody, Fab fragment, Light Chain
B: Maltose binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9076
Polymers92,6873
Non-polymers2203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-45 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.830, 120.810, 193.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resid 2 through 56 or resid 58 through 190 or resid 192 through 228))
21(chain H and (resid 2 through 56 or resid 58...
12(chain A and (resid 1 through 21 or resid 23...
22(chain B and ((resid 1 and (name N or name...
13(chain D and (resid 7 through 23 or (resid 24...
23(chain L and (resid 7 through 89 or resid 91...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain C and (resid 2 through 56 or resid 58 through 190 or resid 192 through 228))C2 - 56
121(chain C and (resid 2 through 56 or resid 58 through 190 or resid 192 through 228))C58 - 190
131(chain C and (resid 2 through 56 or resid 58 through 190 or resid 192 through 228))C192 - 228
211(chain H and (resid 2 through 56 or resid 58...H2 - 56
221(chain H and (resid 2 through 56 or resid 58...H58 - 139
231(chain H and (resid 2 through 56 or resid 58...H141 - 190
241(chain H and (resid 2 through 56 or resid 58...H192 - 228
112(chain A and (resid 1 through 21 or resid 23...A1 - 21
122(chain A and (resid 1 through 21 or resid 23...A23 - 238
132(chain A and (resid 1 through 21 or resid 23...A239
142(chain A and (resid 1 through 21 or resid 23...A1 - 366
152(chain A and (resid 1 through 21 or resid 23...A1 - 366
162(chain A and (resid 1 through 21 or resid 23...A1 - 366
172(chain A and (resid 1 through 21 or resid 23...A1 - 366
212(chain B and ((resid 1 and (name N or name...B1
222(chain B and ((resid 1 and (name N or name...B1 - 366
232(chain B and ((resid 1 and (name N or name...B1 - 366
242(chain B and ((resid 1 and (name N or name...B1 - 366
252(chain B and ((resid 1 and (name N or name...B1 - 366
113(chain D and (resid 7 through 23 or (resid 24...D7 - 23
123(chain D and (resid 7 through 23 or (resid 24...D24 - 25
133(chain D and (resid 7 through 23 or (resid 24...D7 - 215
143(chain D and (resid 7 through 23 or (resid 24...D7 - 215
153(chain D and (resid 7 through 23 or (resid 24...D7 - 215
163(chain D and (resid 7 through 23 or (resid 24...D7 - 215
213(chain L and (resid 7 through 89 or resid 91...L7 - 89
223(chain L and (resid 7 through 89 or resid 91...L91 - 162
233(chain L and (resid 7 through 89 or resid 91...L164 - 194
243(chain L and (resid 7 through 89 or resid 91...L196 - 215

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#3: Protein Maltose binding protein / Maltose-binding protein


Mass: 44175.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pHFT2 / Details (production host): N-terminal 10XHis, FLag, TEV / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9*PLUS

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Antibody , 2 types, 4 molecules HCLD

#1: Antibody Synthetic antibody, Fab fragment, Heavy Chain /


Mass: 25251.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRH2.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Antibody Synthetic antibody, Fab fragment, Light Chain /


Mass: 23260.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 987 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 984 / 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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.2 M NaCl, 0.1 M sodium/potassium phosphate: pH 6.4 and 24% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→19.806 Å / Num. obs: 97817 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.961 % / Biso Wilson estimate: 33.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.121 / Χ2: 1.027 / Net I/σ(I): 10.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.24.0630.891.6464890.6041.025100
2.2-2.34.0760.7421.98112910.6450.855100
2.3-2.44.0820.5632.5996040.7640.64999.9
2.4-2.54.0920.4483.2280440.8390.51699.9
2.5-34.0640.2345.85262400.9510.2799.9
3-43.8330.07215.31207580.9930.08498.5
4-53.5760.04323.8872970.9960.05196.1
5-63.720.03726.6132980.9970.04397.1
6-103.880.02734.7637000.9990.03198.9
10-19.8063.630.01646.75109610.01998

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
MD2data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OMP, 3PGF

1omp

3pgf


Resolution: 2.15→19.806 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7
RfactorNum. reflection% reflection
Rfree0.2531 4857 4.97 %
Rwork0.2054 --
obs0.2078 97669 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 179.23 Å2 / Biso mean: 38.9834 Å2 / Biso min: 17.21 Å2
Refinement stepCycle: final / Resolution: 2.15→19.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12220 0 13 984 13217
Biso mean--55.43 39.99 -
Num. residues----1604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312588
X-RAY DIFFRACTIONf_angle_d0.59217150
X-RAY DIFFRACTIONf_chiral_restr0.0431898
X-RAY DIFFRACTIONf_plane_restr0.0052208
X-RAY DIFFRACTIONf_dihedral_angle_d11.4897515
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C1988X-RAY DIFFRACTION7.488TORSIONAL
12H1988X-RAY DIFFRACTION7.488TORSIONAL
21A3404X-RAY DIFFRACTION7.488TORSIONAL
22B3404X-RAY DIFFRACTION7.488TORSIONAL
31D1815X-RAY DIFFRACTION7.488TORSIONAL
32L1815X-RAY DIFFRACTION7.488TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.17440.33161510.293630573208100
2.1744-2.20.2961600.288531163276100
2.2-2.22670.3551620.284130363198100
2.2267-2.25490.37791440.28931063250100
2.2549-2.28450.36561630.298530733236100
2.2845-2.31580.34541790.278330833262100
2.3158-2.34880.35481590.271731013260100
2.3488-2.38380.33351630.262230833246100
2.3838-2.4210.31921600.254430893249100
2.421-2.46060.30261940.253830403234100
2.4606-2.5030.32921420.245831303272100
2.503-2.54840.311770.243830713248100
2.5484-2.59730.28111590.240530923251100
2.5973-2.65020.34761600.246131073267100
2.6502-2.70770.30391600.239530823242100
2.7077-2.77050.31491730.241930833256100
2.7705-2.83960.28221600.233531073267100
2.8396-2.91610.28381850.240230633248100
2.9161-3.00170.29811690.230631133282100
3.0017-3.09820.27951490.219431343283100
3.0982-3.20850.23341630.21243096325999
3.2085-3.33640.25481740.21023088326299
3.3364-3.48740.23631500.19793087323798
3.4874-3.67020.23411570.19363055321298
3.6702-3.89850.25531810.18623046322798
3.8985-4.19690.19831380.16993060319897
4.1969-4.61440.1931650.14713043320896
4.6144-5.27110.19021500.1473059320996
5.2711-6.59990.19451500.17053159330998
6.5999-19.80640.16841600.15993353351399
Refinement TLS params.Method: refined / Origin x: 40.6323 Å / Origin y: 5.8194 Å / Origin z: -69.2155 Å
111213212223313233
T0.1711 Å2-0.0016 Å2-0.0078 Å2-0.2136 Å20.0078 Å2--0.227 Å2
L0.0533 °2-0.0156 °20.0438 °2-0.1764 °2-0.0133 °2--0.1933 °2
S0.0122 Å °0.0054 Å °-0.0163 Å °-0.0174 Å °0.0017 Å °-0.0087 Å °0.0186 Å °0.0086 Å °-0.0086 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH2 - 228
2X-RAY DIFFRACTION1allL6 - 215
3X-RAY DIFFRACTION1allC2 - 228
4X-RAY DIFFRACTION1allD7 - 215
5X-RAY DIFFRACTION1allA1 - 366
6X-RAY DIFFRACTION1allB1 - 366
7X-RAY DIFFRACTION1allS1 - 1009
8X-RAY DIFFRACTION1allE2
9X-RAY DIFFRACTION1allF1 - 2

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