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- PDB-5h7q: Crystal structure of human MNDA PYD domain with MBP tag -

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Basic information

Entry
Database: PDB / ID: 5h7q
TitleCrystal structure of human MNDA PYD domain with MBP tag
ComponentsMNDA PYD domain with MBP tag
KeywordsSUGAR BINDING PROTEIN / MNDA / PYD domain / MBP / fusion tag
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
PAAD/DAPIN/Pyrin 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 / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / ACETATE ION / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 Å
AuthorsJin, T.C. / Xiao, T.S.
CitationJournal: Sci Rep / Year: 2017
Title: Design of an expression system to enhance MBP-mediated crystallization
Authors: Jin, T.C. / Chuenchor, W. / Jiang, J. / Cheng, J. / Li, Y. / Fang, K. / Huang, M. / Smith, P. / Xiao, T.S.
History
DepositionNov 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
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 2.1Nov 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

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Assembly

Deposited unit
A: MNDA PYD domain with MBP tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4834
Polymers53,0231
Non-polymers4603
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-0 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.040, 68.810, 174.460
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 MNDA PYD domain with MBP tag


Mass: 53022.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: 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.: 1
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 / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG 4000, 0.1M Tris-HCl pH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 89636 / % possible obs: 98.9 % / Redundancy: 5.9 % / CC1/2: 0.999 / Net I/σ(I): 23.1
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.8 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ifp

4ifp


Resolution: 1.451→40.87 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.69
RfactorNum. reflection% reflection
Rfree0.2248 2000 2.23 %
Rwork0.2074 --
obs0.2078 89607 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.451→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 31 470 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053780
X-RAY DIFFRACTIONf_angle_d0.7925127
X-RAY DIFFRACTIONf_dihedral_angle_d2.8762270
X-RAY DIFFRACTIONf_chiral_restr0.07573
X-RAY DIFFRACTIONf_plane_restr0.005656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.451-1.48730.34351320.3155771X-RAY DIFFRACTION93
1.4873-1.52750.30511410.2916172X-RAY DIFFRACTION99
1.5275-1.57240.32231410.27056194X-RAY DIFFRACTION99
1.5724-1.62320.29031420.26066231X-RAY DIFFRACTION100
1.6232-1.68120.27131440.24986268X-RAY DIFFRACTION100
1.6812-1.74850.27511420.24796260X-RAY DIFFRACTION100
1.7485-1.82810.29511430.25376249X-RAY DIFFRACTION100
1.8281-1.92450.27911430.23746270X-RAY DIFFRACTION100
1.9245-2.04510.25691420.22766221X-RAY DIFFRACTION99
2.0451-2.20290.24751440.21936289X-RAY DIFFRACTION99
2.2029-2.42460.22321430.21726286X-RAY DIFFRACTION99
2.4246-2.77540.24661460.21376356X-RAY DIFFRACTION99
2.7754-3.49640.19971450.19456384X-RAY DIFFRACTION99
3.4964-40.88630.18241520.17256656X-RAY DIFFRACTION99

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