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- PDB-5e7u: MBP-MamC loop structure, a magnetite biomineralizing protein from... -

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Basic information

Entry
Database: PDB / ID: 5e7u
TitleMBP-MamC loop structure, a magnetite biomineralizing protein from Magnetospirillium magneticum AMB-1
ComponentsMaltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein
KeywordsMagnetite binding protein / Magnetite binding / mineralization / MBP / transport protein
Function / homology
Function and homology information


magnetosome membrane / detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / 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 / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / 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 / metal ion binding
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 (E. coli)
Magnetospirillum magneticum AMB-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNudelman, H. / Zarivach, R.
CitationJournal: To Be Published
Title: MBP-MamC loop structure, a magnetite biomineralizing protein from Magnetospirillium magneticum AMB-1
Authors: Nudelman, H. / Zarivach, R.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
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_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8215
Polymers45,1911
Non-polymers6304
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-32 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.600, 66.600, 211.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 / MBP / MMBP / Maltodextrin-binding protein / Magnetite ...MBP / MMBP / Maltodextrin-binding protein / MBP / MMBP / Maltodextrin-binding protein / Magnetite binding protein


Mass: 45190.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (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.: 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
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate , 2 M Ammonium sulfate / PH range: 3.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.8→63.52 Å / Num. obs: 11938 / % possible obs: 95.23 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 24.64
Reflection shellRedundancy: 8.3 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 4.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PUZ

3puz


Resolution: 2.8→63.52 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.827 / SU B: 49.523 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30725 596 5 %RANDOM
Rwork0.26747 ---
obs0.26958 11241 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.074 Å2
Baniso -1Baniso -2Baniso -3
1-4.27 Å2-0 Å2-0 Å2
2--4.27 Å2-0 Å2
3----8.55 Å2
Refinement stepCycle: 1 / Resolution: 2.8→63.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 38 16 3006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.023057
X-RAY DIFFRACTIONr_bond_other_d0.0010.022906
X-RAY DIFFRACTIONr_angle_refined_deg0.8371.9794151
X-RAY DIFFRACTIONr_angle_other_deg0.68636735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5865379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03825.954131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57315517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.901156
X-RAY DIFFRACTIONr_chiral_restr0.0480.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0213423
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02637
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_it0.1742.8971519
X-RAY DIFFRACTIONr_mcbond_other0.1742.8971518
X-RAY DIFFRACTIONr_mcangle_it0.3264.3451897
X-RAY DIFFRACTIONr_mcangle_other0.3264.3451898
X-RAY DIFFRACTIONr_scbond_it0.1032.9681538
X-RAY DIFFRACTIONr_scbond_other0.1032.9681538
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.1974.4442255
X-RAY DIFFRACTIONr_long_range_B_refined1.56527.4312624
X-RAY DIFFRACTIONr_long_range_B_other1.56527.42712619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.802→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 50 -
Rwork0.358 833 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 11.225 Å / Origin y: -26.525 Å / Origin z: 16.586 Å
111213212223313233
T0.02 Å2-0.0334 Å20.0098 Å2-0.1371 Å2-0.002 Å2--0.3294 Å2
L0.587 °2-0.1738 °20.5305 °2-0.8097 °2-0.7633 °2--2.9513 °2
S0.0203 Å °0.0636 Å °-0.0226 Å °0.0482 Å °0.0478 Å °0.0531 Å °0.0243 Å °-0.1786 Å °-0.0681 Å °

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