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- PDB-6eqz: A MamC-MIC insertion in MBP scaffold at position K170 -

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Basic information

Entry
Database: PDB / ID: 6eqz
TitleA MamC-MIC insertion in MBP scaffold at position K170
ComponentsMaltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein
KeywordsMAGNETITE-BINDING PROTEIN / MamC / Magnetotactic bacteria / Magnetite interacting component / Biomineralization / Transport protein
Function / homology
Function and homology information


magnetosome membrane / 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 ...magnetosome membrane / 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 / metal ion binding / 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
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein / Magnetosome protein MamC
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Magnetospirillum magneticum AMB-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.293 Å
AuthorsNudelman, H. / Zarivach, R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The importance of the helical structure of a MamC-derived magnetite-interacting peptide for its function in magnetite formation.
Authors: Nudelman, H. / Perez Gonzalez, T. / Kolushiva, S. / Widdrat, M. / Reichel, V. / Peigneux, A. / Davidov, G. / Bitton, R. / Faivre, D. / Jimenez-Lopez, C. / Zarivach, R.
History
DepositionOct 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 7, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein
B: Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein
D: Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein
G: Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,7038
Polymers175,3344
Non-polymers1,3694
Water5,188288
1
A: Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1762
Polymers43,8331
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1762
Polymers43,8331
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1762
Polymers43,8331
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1762
Polymers43,8331
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.682, 113.813, 115.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 43833.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Magnetospirillum magneticum AMB-1 (bacteria)
Gene: malE, Z5632, ECs5017, mms13, amb0951 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEY0, UniProt: Q2W8S0, 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.: 4
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


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1,86 M Tris-Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.29→46.7 Å / Num. obs: 65839 / % possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.252 / Net I/σ(I): 5.5
Reflection shellResolution: 2.29→2.35 Å / Rmerge(I) obs: 2.133

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E7U

5e7u


Resolution: 2.293→46.696 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.52
RfactorNum. reflection% reflection
Rfree0.2738 3320 5.07 %
Rwork0.2046 --
obs0.2082 65508 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.293→46.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11645 0 92 288 12025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912069
X-RAY DIFFRACTIONf_angle_d1.19316407
X-RAY DIFFRACTIONf_dihedral_angle_d4.6548599
X-RAY DIFFRACTIONf_chiral_restr0.0631828
X-RAY DIFFRACTIONf_plane_restr0.0072116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2929-2.32570.37321140.32962304X-RAY DIFFRACTION89
2.3257-2.36040.4061160.31532532X-RAY DIFFRACTION97
2.3604-2.39730.32711360.29362589X-RAY DIFFRACTION100
2.3973-2.43660.34341500.30152524X-RAY DIFFRACTION100
2.4366-2.47860.41281330.32192571X-RAY DIFFRACTION99
2.4786-2.52370.4761290.34192568X-RAY DIFFRACTION99
2.5237-2.57220.38771460.29892568X-RAY DIFFRACTION100
2.5722-2.62470.34871470.27282578X-RAY DIFFRACTION100
2.6247-2.68180.35211400.25942559X-RAY DIFFRACTION100
2.6818-2.74420.36321530.26362580X-RAY DIFFRACTION100
2.7442-2.81280.31141170.24592607X-RAY DIFFRACTION100
2.8128-2.88880.31571540.24922595X-RAY DIFFRACTION100
2.8888-2.97380.29911390.24182572X-RAY DIFFRACTION100
2.9738-3.06980.34851740.22822580X-RAY DIFFRACTION100
3.0698-3.17950.29851290.21342596X-RAY DIFFRACTION100
3.1795-3.30670.3241530.20082593X-RAY DIFFRACTION100
3.3067-3.45720.24531420.17872605X-RAY DIFFRACTION100
3.4572-3.63940.21181040.15792630X-RAY DIFFRACTION100
3.6394-3.86730.22741730.15712603X-RAY DIFFRACTION100
3.8673-4.16570.1851290.1422639X-RAY DIFFRACTION100
4.1657-4.58460.2218960.14162673X-RAY DIFFRACTION100
4.5846-5.24720.1881770.15282620X-RAY DIFFRACTION100
5.2472-6.6080.28761330.19332694X-RAY DIFFRACTION100
6.608-46.70520.22821360.18882808X-RAY DIFFRACTION99
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)
10.5916-0.25490.05580.64710.07310.72590.0166-0.0165-0.02090.0081-0.02890.0868-0.0061-0.13980.02330.24390.0214-0.00730.4591-0.02070.357134.0065113.14151.0509
20.47290.25-0.1030.62290.10221.0005-0.01550.08070.0202-0.0294-0.02270.0289-0.0299-0.02240.02350.16810.01-0.01080.4004-0.00920.242676.5225112.831.7771
30.770.7206-0.29931.1944-0.48310.18480.0439-0.1884-0.08610.1594-0.0714-0.096-0.08680.04780.03120.22860.0043-0.0140.41820.03760.25862.312687.728628.5393
41.49230.1998-0.39151.4244-0.32990.8668-0.01480.1925-0.2068-0.1526-0.0619-0.0439-0.05990.02150.08420.1742-0.0181-0.02740.3992-0.04170.306848.142187.937-25.6364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 3:379)
2X-RAY DIFFRACTION2(chain B and resseq 3:379)
3X-RAY DIFFRACTION3(chain D and resseq 1:379)
4X-RAY DIFFRACTION4(chain G and resseq 2:379)

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