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- PDB-4r0y: Structure of Maltose-binding Protein Fusion with the C-terminal G... -

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Basic information

Entry
Database: PDB / ID: 4r0y
TitleStructure of Maltose-binding Protein Fusion with the C-terminal GH1 domain of Guanylate Kinase-associated Protein from Rattus norvegicus
ComponentsMaltose-binding periplasmic protein, Disks large-associated protein 1
KeywordsPROTEIN BINDING / three-helix bundle / synaptic scaffolding protein
Function / homology
Function and homology information


maintenance of postsynaptic density structure / postsynaptic specialization / Neurexins and neuroligins / signaling / structural constituent of postsynaptic density / protein localization to synapse / aggresome assembly / detection of maltose stimulus / maltose transport complex / maltose binding ...maintenance of postsynaptic density structure / postsynaptic specialization / Neurexins and neuroligins / signaling / structural constituent of postsynaptic density / protein localization to synapse / aggresome assembly / 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 / postsynaptic density, intracellular component / regulation of proteasomal protein catabolic process / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / modulation of chemical synaptic transmission / outer membrane-bounded periplasmic space / postsynaptic membrane / postsynaptic density / periplasmic space / molecular adaptor activity / protein domain specific binding / glutamatergic synapse / synapse / DNA damage response / protein-containing complex binding / membrane / plasma membrane
Similarity search - Function
SAPAP family / Guanylate-kinase-associated protein (GKAP) protein / 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
Maltose/maltodextrin-binding periplasmic protein / Disks large-associated protein 1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIm, Y.J. / Tong, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus.
Authors: Tong, J. / Yang, H. / Eom, S.H. / Chun, C. / Im, Y.J.
History
DepositionAug 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: 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 periplasmic protein, Disks large-associated protein 1
B: Maltose-binding periplasmic protein, Disks large-associated protein 1


Theoretical massNumber of molelcules
Total (without water)112,4352
Polymers112,4352
Non-polymers00
Water3,261181
1
A: Maltose-binding periplasmic protein, Disks large-associated protein 1


Theoretical massNumber of molelcules
Total (without water)56,2181
Polymers56,2181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein, Disks large-associated protein 1


Theoretical massNumber of molelcules
Total (without water)56,2181
Polymers56,2181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.110, 158.676, 65.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Maltose-binding periplasmic protein, Disks large-associated protein 1 / MBP / MMBP / Maltodextrin-binding protein / DAP-1 / Guanylate kinase-associated protein / rGKAP / ...MBP / MMBP / Maltodextrin-binding protein / DAP-1 / Guanylate kinase-associated protein / rGKAP / PSD-95/SAP90-binding protein 1 / SAP90/PSD-95-associated protein 1 / SAPAP1


Mass: 56217.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion protein of N-terminal residues 1-361 from Maltose-binding periplasmic protein (P0AEX9, MALE_ECOLI), linker residues (AM), residues 807-971 from Disks large-associated protein 1 ...Details: Fusion protein of N-terminal residues 1-361 from Maltose-binding periplasmic protein (P0AEX9, MALE_ECOLI), linker residues (AM), residues 807-971 from Disks large-associated protein 1 (P97836, DLGP1_RAT) with loop deletion of residue 917-945, the loop was replaced with residues VD.
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Rattus norvegicus (Norway rat)
Plasmid: pHMBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9, UniProt: P97836
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Sodium Citrate pH 5.0, 15% PEG 1500, 0.1M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 2, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 72320 / Num. obs: 68103 / % possible obs: 97.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.9 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 45.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 3.92 / Num. unique all: 2793 / % possible all: 80.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OMP

1omp


Resolution: 2→39.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2315270.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3452 5.1 %RANDOM
Rwork0.243 ---
all0.265 68103 --
obs0.243 67943 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.7122 Å2 / ksol: 0.367904 e/Å3
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1-11.15 Å20 Å20 Å2
2--7.76 Å20 Å2
3----18.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7430 0 0 181 7611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 503 5.2 %
Rwork0.324 9097 -
obs--82.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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