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- PDB-1mh4: maltose binding-a1 homeodomain protein chimera, crystal form II -

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Basic information

Entry
Database: PDB / ID: 1mh4
Titlemaltose binding-a1 homeodomain protein chimera, crystal form II
Componentsmaltose binding-a1 homeodomain protein chimera
KeywordsSUGAR BINDING / DNA BINDING PROTEIN / MATa1 / homeodomain / binding cooperativity / maltose binding protein / MBP
Function / homology
Function and homology information


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 ...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 / DNA-binding transcription factor activity, RNA polymerase II-specific / periplasmic space / DNA damage response / DNA binding / nucleus / membrane
Similarity search - Function
Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Homeodomain-like ...Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Homeodomain-like / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / Homeobox-like domain superfamily / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mating-type protein A1 / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKe, A. / Wolberger, C.
CitationJournal: Protein Sci. / Year: 2003
Title: Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera
Authors: Ke, A. / Wolberger, C.
History
DepositionAug 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: maltose binding-a1 homeodomain protein chimera


Theoretical massNumber of molelcules
Total (without water)46,4041
Polymers46,4041
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.254, 88.705, 96.159
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-a1 homeodomain protein chimera / MATa1 homeodomain-maltose binding protein chimera


Mass: 46403.832 Da / Num. of mol.: 1 / Mutation: E359A, K362A, D363A
Source method: isolated from a genetically manipulated source
Details: Chimera consisting of residues 1-366 (sequence database residues 27-392) of Maltose-binding periplasmic protein, a 5 alanine linker, and residues 477-526 (sequence database residues 77-126) ...Details: Chimera consisting of residues 1-366 (sequence database residues 27-392) of Maltose-binding periplasmic protein, a 5 alanine linker, and residues 477-526 (sequence database residues 77-126) of homeobox of mating-type protein A-1.
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Genus: Escherichia, Saccharomyces / Species: , / Strain: , / Plasmid: pMAL-c2 with modifications at the fusion linker / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus
References: UniProt: P02928, UniProt: P01366, UniProt: P0AEX9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
2100 mMMES1reservoirpH6.0
320 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2000
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→44.54 Å / Num. all: 19730 / Num. obs: 19118 / % possible obs: 0.969 % / Observed criterion σ(F): 3.58 / Observed criterion σ(I): 3.58 / Redundancy: 9.97 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 22.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 3.58 / Rsym value: 0.24 / % possible all: 83.2
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 96.9 %
Reflection shell
*PLUS
% possible obs: 83.2 % / Rmerge(I) obs: 0.24

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code: 4MBP

4mbp


Resolution: 2.3→44.54 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3.58 / σ(I): 3.58 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 973 5.1 %RANDOM
Rwork0.243 ---
all-19730 --
obs-19118 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.5153 Å2 / ksol: 0.316721 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-9.85 Å20 Å20 Å2
2---5.74 Å20 Å2
3----4.11 Å2
Refine analyzeLuzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 0 138 3333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 148 5.2 %
Rwork0.273 2683 -
obs--88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.264
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0064
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.37

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