[English] 日本語
Yorodumi
- PDB-5mm3: Unstructured MamC magnetite-binding protein located between two h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mm3
TitleUnstructured MamC magnetite-binding protein located between two helices.
ComponentsSugar ABC transporter substrate-binding protein,Magnetosome protein MamC,Sugar ABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / Magnetosom / Magnetotactic bacteria / MamC / Magnetite / Biomineralization / Protein-mineral interaction
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane 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
Similarity search - Function
Pectin lyase fold/virulence factor / 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 / Maltodextrin-binding protein / Magnetosome protein MamC / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
Magnetospirillum sp. XM-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionDec 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
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 / Category: citation / citation_author
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
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sugar ABC transporter substrate-binding protein,Magnetosome protein MamC,Sugar ABC transporter substrate-binding protein
B: Sugar ABC transporter substrate-binding protein,Magnetosome protein MamC,Sugar ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0664
Polymers90,3822
Non-polymers6852
Water5,278293
1
A: Sugar ABC transporter substrate-binding protein,Magnetosome protein MamC,Sugar ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5332
Polymers45,1911
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sugar ABC transporter substrate-binding protein,Magnetosome protein MamC,Sugar ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5332
Polymers45,1911
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.285, 115.285, 117.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

21B-602-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 351 / Label seq-ID: 22 - 372

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Sugar ABC transporter substrate-binding protein,Magnetosome protein MamC,Sugar ABC transporter substrate-binding protein


Mass: 45190.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea), (gene. exp.) Magnetospirillum sp. XM-1 (magnetotactic)
Gene: malE, DU73_08550, mamC, XM1_2330 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F8QGU4, UniProt: A0A0U5I168, 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.: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.4 M tri-Sodium citrate and 0.1 M HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.1→82.18 Å / Num. obs: 38573 / % possible obs: 82.6 % / Redundancy: 3 % / Rrim(I) all: 0.118 / Net I/σ(I): 23.3
Reflection shellRedundancy: 2.9 % / Mean I/σ(I) obs: 4.56 / Rrim(I) all: 0.43 / % possible all: 87.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Cootmodel building
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E7U

5e7u


Resolution: 2.1→82.18 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.177 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22781 1920 5 %RANDOM
Rwork0.18216 ---
obs0.18445 36623 82.63 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 32.307 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å2-0 Å2-0 Å2
2--2.03 Å2-0 Å2
3----4.06 Å2
Refinement stepCycle: 1 / Resolution: 2.1→82.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5617 0 46 293 5956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025819
X-RAY DIFFRACTIONr_bond_other_d0.0060.025536
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9747906
X-RAY DIFFRACTIONr_angle_other_deg1.262312833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64425.92250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04715975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0161510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216552
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021226
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_it2.4021.6362897
X-RAY DIFFRACTIONr_mcbond_other2.4011.6362896
X-RAY DIFFRACTIONr_mcangle_it3.232.443620
X-RAY DIFFRACTIONr_mcangle_other3.232.4413621
X-RAY DIFFRACTIONr_scbond_it4.0392.0732922
X-RAY DIFFRACTIONr_scbond_other4.0382.0732922
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8222.9144286
X-RAY DIFFRACTIONr_long_range_B_refined7.34714.1476825
X-RAY DIFFRACTIONr_long_range_B_other7.35613.9596739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 42356 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 146 -
Rwork0.234 2800 -
obs--87.11 %
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)
10.85820.0873-0.0261.38010.5250.85320.0231-0.02990.00030.0765-0.03890.02340.0214-0.11050.01580.0116-0.01580.00470.07430.00720.09052.75235.24313.347
21.07550.38820.26670.984-0.19211.38690.0125-0.15780.0170.14930.0598-0.1225-0.06930.0665-0.07230.04870.0123-0.01510.1192-0.05710.163139.37926.88124.267
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 371
2X-RAY DIFFRACTION2B1 - 352

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more