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- PDB-5bjz: Crystal structure of maltose binding protein in complex with an a... -

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Basic information

Entry
Database: PDB / ID: 5bjz
TitleCrystal structure of maltose binding protein in complex with an allosteric synthetic antibody
Components
  • (Synthetic antibody, Fab fragment, ...) x 2
  • Maltose-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN / Maltose binding protein / conformation specific synthetic antibody
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / outer membrane-bounded periplasmic space
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 speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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 / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)187,47816
Polymers186,0246
Non-polymers1,45410
Water20,8971160
1
B: Maltose-binding periplasmic protein
D: Synthetic antibody, Fab fragment, Heavy Chain
H: Synthetic antibody, Fab fragment, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9049
Polymers93,0123
Non-polymers8926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-50 kcal/mol
Surface area34110 Å2
MethodPISA
2
C: Synthetic antibody, Fab fragment, Heavy Chain
L: Synthetic antibody, Fab fragment, Light Chain
A: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5747
Polymers93,0123
Non-polymers5624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-56 kcal/mol
Surface area33980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.390, 87.590, 114.650
Angle α, β, γ (deg.)90.000, 114.290, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 41 or resid 43...
21(chain B and (resid 1 through 41 or resid 43...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASPASP(chain A and (resid 1 through 41 or resid 43...AD1 - 4132 - 72
12LEULEULEULEU(chain A and (resid 1 through 41 or resid 43...AD43 - 10374 - 134
13ALAALAASPASP(chain A and (resid 1 through 41 or resid 43...AD105 - 136136 - 167
14GLUGLUGLUGLU(chain A and (resid 1 through 41 or resid 43...AD138 - 172169 - 203
15GLYGLYALAALA(chain A and (resid 1 through 41 or resid 43...AD174 - 188205 - 219
16ALAALATRPTRP(chain A and (resid 1 through 41 or resid 43...AD190 - 232221 - 263
17ASNASNSERSER(chain A and (resid 1 through 41 or resid 43...AD234 - 238265 - 269
18VALVALLYSLYS(chain A and (resid 1 through 41 or resid 43...AD240 - 273271 - 304
19LEULEUALAALA(chain A and (resid 1 through 41 or resid 43...AD275 - 364306 - 395
21LYSLYSASPASP(chain B and (resid 1 through 41 or resid 43...BA1 - 4132 - 72
22LEULEULEULEU(chain B and (resid 1 through 41 or resid 43...BA43 - 10374 - 134
23ALAALAASPASP(chain B and (resid 1 through 41 or resid 43...BA105 - 136136 - 167
24GLUGLUGLUGLU(chain B and (resid 1 through 41 or resid 43...BA138 - 172169 - 203
25GLYGLYALAALA(chain B and (resid 1 through 41 or resid 43...BA174 - 188205 - 219
26ALAALATRPTRP(chain B and (resid 1 through 41 or resid 43...BA190 - 232221 - 263
27ASNASNSERSER(chain B and (resid 1 through 41 or resid 43...BA234 - 238265 - 269
28VALVALLYSLYS(chain B and (resid 1 through 41 or resid 43...BA240 - 273271 - 304
29LEULEUALAALA(chain B and (resid 1 through 41 or resid 43...BA275 - 364306 - 395

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Components

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Antibody , 2 types, 4 molecules CDLH

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


Mass: 25482.318 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
#3: Antibody Synthetic antibody, Fab fragment, Light Chain /


Mass: 23353.967 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

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Protein / Sugars , 2 types, 4 molecules BA

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


Mass: 44175.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: malE, Z5632, ECs5017 / Plasmid: pHFT2 / Details (production host): N-terminal 10xHis, Flag, TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AEY0
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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 , 4 types, 1168 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1160 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES: pH 7.0 and 15% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→19.957 Å / Num. obs: 126257 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.316 % / Biso Wilson estimate: 31.63 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.091 / Χ2: 1.043 / Net I/σ(I): 9.85
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-23.4140.8961.7592540.6421.06698.2
2-2.23.2770.552.75287930.8240.6696.9
2.2-2.43.4370.285.24203440.9330.33498.6
2.4-2.53.410.1827.278530.9680.21798.6
2.5-33.2780.10310.23250580.9880.12496.8
3-43.2530.05417.29200780.9950.06597.4
4-53.1920.04123.1871500.9960.04997
5-63.370.03626.0532570.9970.04399
6-103.2210.03327.9234590.9970.03996.8
10-19.9573.5750.03334.0710110.9960.03998.2

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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: 3PGF

3pgf


Resolution: 1.95→19.957 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.62
RfactorNum. reflection% reflection
Rfree0.2291 6258 4.96 %
Rwork0.1941 --
obs0.1959 126099 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.51 Å2 / Biso mean: 38.0961 Å2 / Biso min: 16.32 Å2
Refinement stepCycle: final / Resolution: 1.95→19.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12359 0 93 1160 13612
Biso mean--42.68 41.26 -
Num. residues----1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612965
X-RAY DIFFRACTIONf_angle_d0.76917693
X-RAY DIFFRACTIONf_chiral_restr0.051976
X-RAY DIFFRACTIONf_plane_restr0.0052249
X-RAY DIFFRACTIONf_dihedral_angle_d11.1537857
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3342X-RAY DIFFRACTION3.73TORSIONAL
12B3342X-RAY DIFFRACTION3.73TORSIONAL
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 (%)
1.95-1.97210.37381940.32854021421598
1.9721-1.99530.36572590.32243967422699
1.9953-2.01960.36582250.30453907413298
2.0196-2.04520.38472080.29894029423798
2.0452-2.07210.35242130.28984001421499
2.0721-2.10040.32222380.27763965420398
2.1004-2.13040.31621980.26624021421998
2.1304-2.16210.30261960.26183932412897
2.1621-2.19590.25961990.2523805400493
2.1959-2.23180.29432090.24283948415797
2.2318-2.27030.26321810.23264028420999
2.2703-2.31150.29672190.22744095431499
2.3115-2.35590.27671880.22684018420699
2.3559-2.40390.26552200.22384024424499
2.4039-2.45610.29172080.22184019422799
2.4561-2.51310.28092250.22453989421498
2.5131-2.57580.25711970.22054039423698
2.5758-2.64530.26252060.20673998420498
2.6453-2.7230.23652240.20313946417097
2.723-2.81060.24021900.20543905409595
2.8106-2.91080.25252290.20343894412396
2.9108-3.0270.2321950.19464030422598
3.027-3.16420.24322110.19534015422698
3.1642-3.33030.22831940.19044017421198
3.3303-3.53790.2182090.18014055426498
3.5379-3.80930.20132110.17213973418497
3.8093-4.18950.17021800.15533871405194
4.1895-4.78840.15451980.13794099429799
4.7884-6.00540.15992150.15364124433999
6.0054-19.95810.17742190.15774106432597
Refinement TLS params.Method: refined / Origin x: -16.8517 Å / Origin y: -6.5772 Å / Origin z: 123.1373 Å
111213212223313233
T0.2664 Å2-0.0002 Å20.0377 Å2-0.2964 Å2-0.0128 Å2--0.2425 Å2
L-0.0343 °20.0146 °20.2388 °2-0.0121 °2-0.0059 °2--0.2983 °2
S-0.0165 Å °0.0487 Å °-0.0178 Å °-0.0037 Å °0.0016 Å °-0.0042 Å °0.0114 Å °0.1336 Å °0.0129 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1 - 365
2X-RAY DIFFRACTION1allH4 - 233
3X-RAY DIFFRACTION1allL4 - 216
4X-RAY DIFFRACTION1allA1 - 367
5X-RAY DIFFRACTION1allC3 - 233
6X-RAY DIFFRACTION1allD4 - 216
7X-RAY DIFFRACTION1allE1 - 2
8X-RAY DIFFRACTION1allF2 - 6
9X-RAY DIFFRACTION1allS1 - 1179
10X-RAY DIFFRACTION1allG1 - 2
11X-RAY DIFFRACTION1allI1

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