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- PDB-4h1g: Structure of Candida albicans Kar3 motor domain fused to maltose-... -

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Basic information

Entry
Database: PDB / ID: 4h1g
TitleStructure of Candida albicans Kar3 motor domain fused to maltose-binding protein
ComponentsMaltose binding protein-CaKar3 motor domain fusion protein
KeywordsMOTOR PROTEIN / Kinesin motor domain / chimera
Function / homology
Function and homology information


microtubule motor activity / detection of maltose stimulus / maltose transport complex / microtubule-based movement / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...microtubule motor activity / detection of maltose stimulus / maltose transport complex / microtubule-based movement / 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 / microtubule binding / microtubule / periplasmic space / DNA damage response / ATP binding / membrane
Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / 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 / Kinesin motor domain superfamily / Bacterial extracellular solute-binding protein / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltotetraose / ADENOSINE-5'-DIPHOSPHATE / Kinesin-like protein / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Candida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsAllingham, J.A. / Duan, D. / Delorme, C. / Joshi, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structure of the Candida albicans Kar3 kinesin motor domain fused to maltose-binding protein.
Authors: Delorme, C. / Joshi, M. / Allingham, J.S.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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 / _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.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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 protein-CaKar3 motor domain fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2625
Polymers79,0821
Non-polymers1,1804
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.463, 74.927, 98.673
Angle α, β, γ (deg.)90.000, 96.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltose binding protein-CaKar3 motor domain fusion protein


Mass: 79082.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Candida albicans (yeast)
Strain: MS 21-1,WO-1 / Production host: Escherichia coli (E. coli)
References: UniProt: D8A942, UniProt: C4YKK8, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 393 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT, (1) IN CANDIDA ALBICANS RESIDUE 405 WOULD BE SERINE BECAUSE OF ITS CODON USAGE, ...AUTHORS STATE THAT, (1) IN CANDIDA ALBICANS RESIDUE 405 WOULD BE SERINE BECAUSE OF ITS CODON USAGE, BUT BECAUSE OF RECOMBINANT PROTEIN EXPRESSION IN E. COLI IT WAS TRANSLATED AS LEUCINE; (2) REGARDING RESIDUE 683, THERE MIGHT BE VARIATIONS FROM SOME OF THE PUBLISHED SEQUENCES DUE TO DIFFERENCES IN THE STRAIN OF YEAST SEQUENCED.

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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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 14% PEG 4000, 75 mM NaCl, 5% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→19.9 Å / Num. obs: 38614 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.527 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.02
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.15-2.50.3373.834430414048199.4
2.5-30.1548.323297210357199.2
3-40.05818.69260018204198.5
4-60.03527.67133604235198.1
6-100.02929.1444911426197.9
10-19.90.02235.381058344183.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
Locallymodified Blu-Ice Gui interface to EPICS controldata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3KAR and 1MH3

3kar

1mh3


Resolution: 2.15→19.896 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8631 / SU ML: 0.21 / σ(F): 2 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 1931 5 %random
Rwork0.1692 ---
obs0.1713 38611 98.95 %-
all-38614 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.77 Å2 / Biso mean: 30.7075 Å2 / Biso min: 12.93 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5086 0 77 390 5553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055292
X-RAY DIFFRACTIONf_angle_d0.9327205
X-RAY DIFFRACTIONf_chiral_restr0.06834
X-RAY DIFFRACTIONf_plane_restr0.004919
X-RAY DIFFRACTIONf_dihedral_angle_d12.6871873
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 (%)
2.15-2.20370.27141360.213225842720100
2.2037-2.26320.29071380.203526332771100
2.2632-2.32970.25541380.19932607274599
2.3297-2.40480.23441390.18326392778100
2.4048-2.49060.23631380.18452625276399
2.4906-2.59010.25981380.1822618275699
2.5901-2.70770.24371360.17942600273699
2.7077-2.85010.25271380.19262622276099
2.8501-3.02810.23071390.1872631277099
3.0281-3.26090.24361370.18482612274999
3.2609-3.58740.22981380.16312611274998
3.5874-4.10250.16121380.14422619275799
4.1025-5.15380.13821380.13042622276098
5.1538-19.89650.18181400.16382657279798

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