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- PDB-5jst: MBP fused MDV1 coiled coil -

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Basic information

Entry
Database: PDB / ID: 5jst
TitleMBP fused MDV1 coiled coil
ComponentsMaltose-binding periplasmic protein,Mitochondrial division protein 1
KeywordsPROTEIN BINDING / MBP / Coiled-coil / SER
Function / homology
Function and homology information


U4 snRNA binding / 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 / U6 snRNA binding ...U4 snRNA binding / 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 / U6 snRNA binding / U4/U6 x U5 tri-snRNP complex / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / mRNA splicing, via spliceosome / outer membrane-bounded periplasmic space / mitochondrial outer membrane / periplasmic space / DNA damage response / membrane
Similarity search - Function
Mitochondrial division protein 1 / Mitochondrial division protein 1 / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...Mitochondrial division protein 1 / Mitochondrial division protein 1 / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
alpha-maltose / ACETATE ION / Mitochondrial division protein 1 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsKim, B.-W. / Song, H.K.
CitationJournal: Sci Rep / Year: 2017
Title: ACCORD: an assessment tool to determine the orientation of homodimeric coiled-coils.
Authors: Kim, B.W. / Jung, Y.O. / Kim, M.K. / Kwon, D.H. / Park, S.H. / Kim, J.H. / Kuk, Y.B. / Oh, S.J. / Kim, L. / Kim, B.H. / Yang, W.S. / Song, H.K.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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
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,Mitochondrial division protein 1
B: Maltose-binding periplasmic protein,Mitochondrial division protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,61010
Polymers97,5382
Non-polymers1,0728
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.515, 102.942, 79.267
Angle α, β, γ (deg.)90.000, 102.510, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain B

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Components

#1: Protein Maltose-binding periplasmic protein,Mitochondrial division protein 1 / MBP / MMBP / Maltodextrin-binding protein / Mitochondria fission 2 protein


Mass: 48769.055 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-392,UNP RESIDUES 230-300
Source method: isolated from a genetically manipulated source
Details: The fusion protein of MBP and MDV1 (Mitochondrial division protein 1)
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: K12, YJM789 / Gene: malE, b4034, JW3994, MDV1, FIS2, GAG3, NET2, SCY_3176 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: A6ZQL5
#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: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.3~1.7 M Sodium formate, 25% PEG 3350, 0.1 M CaCl2, 0.1 M Sodium acetate/Acetic acid, pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.2553 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2553 Å / Relative weight: 1
ReflectionResolution: 2.199→50 Å / Num. obs: 50774 / % possible obs: 99.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.036 / Rrim(I) all: 0.072 / Χ2: 2.277 / Net I/av σ(I): 35.927 / Net I/σ(I): 15.4 / Num. measured all: 205521
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.244.10.69725360.6960.3930.8011.438100
2.24-2.284.10.61925320.7580.3480.7111.449100
2.28-2.324.10.51725740.830.290.5941.495100
2.32-2.374.10.42925540.8650.2420.4941.517100
2.37-2.424.10.35925700.90.2010.4121.578100
2.42-2.484.10.31725360.920.1780.3641.575100
2.48-2.544.20.26225200.9380.1460.3011.663100
2.54-2.614.10.21725500.9610.1220.251.706100
2.61-2.694.10.17625490.9720.0980.2021.801100
2.69-2.774.10.13825660.9830.0770.1581.835100
2.77-2.874.10.12225390.9850.0690.1411.997100
2.87-2.994.10.125640.9890.0560.1152.235100
2.99-3.124.10.08825540.9920.0490.1012.49100
3.12-3.294.10.07525690.9930.0420.0863.007100
3.29-3.493.90.06825470.9920.0390.0783.382100
3.49-3.763.80.05825700.9950.0340.0683.80199.8
3.76-4.143.80.05425750.9950.0320.0623.97299.7
4.14-4.743.80.04525190.9960.0270.0533.51398.2
4.74-5.9740.0425590.9970.0220.0462.95699.3
5.97-503.80.03622910.9970.0210.0412.74687.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DM0, 2XU6

3dm0

2xu6


Resolution: 2.199→36.846 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2736 2011 3.96 %
Rwork0.2249 48755 -
obs0.2268 50766 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.05 Å2 / Biso mean: 60.8294 Å2 / Biso min: 31.49 Å2
Refinement stepCycle: final / Resolution: 2.199→36.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 86 221 6836
Biso mean--66.67 55.26 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076737
X-RAY DIFFRACTIONf_angle_d0.8799169
X-RAY DIFFRACTIONf_chiral_restr0.0551041
X-RAY DIFFRACTIONf_plane_restr0.0061192
X-RAY DIFFRACTIONf_dihedral_angle_d11.4874011
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3484X-RAY DIFFRACTION7.342TORSIONAL
12B3484X-RAY DIFFRACTION7.342TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1989-2.25390.39611430.333440358399
2.2539-2.31480.33841500.302234943644100
2.3148-2.38290.36341440.291435053649100
2.3829-2.45980.35821370.288134913628100
2.4598-2.54770.34781440.286235183662100
2.5477-2.64970.33161400.282535213661100
2.6497-2.77020.29291390.275834933632100
2.7702-2.91620.31921440.280635053649100
2.9162-3.09880.34671460.284435073653100
3.0988-3.3380.31691540.262135093663100
3.338-3.67360.28631420.230935063648100
3.6736-4.20450.24651460.197235083654100
4.2045-5.29470.22791460.17063480362698
5.2947-36.85070.21171360.18043278341491

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