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- PDB-5wq6: Crystal Structure of hMNDA-PYD with MBP tag -

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Basic information

Entry
Database: PDB / ID: 5wq6
TitleCrystal Structure of hMNDA-PYD with MBP tag
ComponentsMBP tagged hMNDA-PYD
KeywordsSUGAR BINDING PROTEIN / PYD / death fold / MBP / crystallization 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
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: 1.648 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 23, 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 / pdbx_struct_assembly_gen / 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.pdbx_formal_charge / _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.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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: MBP tagged hMNDA-PYD
B: MBP tagged hMNDA-PYD
C: MBP tagged hMNDA-PYD
D: MBP tagged hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,44816
Polymers210,5894
Non-polymers1,86012
Water35,1111949
1
A: MBP tagged hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1765
Polymers52,6471
Non-polymers5294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint2 kcal/mol
Surface area20380 Å2
MethodPISA
2
B: MBP tagged hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0483
Polymers52,6471
Non-polymers4012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint2 kcal/mol
Surface area19960 Å2
MethodPISA
3
C: MBP tagged hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1765
Polymers52,6471
Non-polymers5294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint2 kcal/mol
Surface area19950 Å2
MethodPISA
4
D: MBP tagged hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0483
Polymers52,6471
Non-polymers4012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint2 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.010, 186.200, 76.380
Angle α, β, γ (deg.)90.00, 89.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MBP tagged hMNDA-PYD


Mass: 52647.152 Da / Num. of mol.: 4
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.: 4
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 1949 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 15% PEG 8000, 0.2M NH4Ac, NaAc pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.648→50 Å / Num. obs: 241934 / % possible obs: 99 % / Redundancy: 3.7 % / CC1/2: 0.998 / Net I/σ(I): 11.7
Reflection shellResolution: 1.648→1.71 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.708 / % possible all: 95.3

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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: 1.648→48.168 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.38
RfactorNum. reflection% reflection
Rfree0.2123 12116 5.01 %
Rwork0.1783 --
obs0.18 241879 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.648→48.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14446 0 124 1949 16519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615101
X-RAY DIFFRACTIONf_angle_d0.80420482
X-RAY DIFFRACTIONf_dihedral_angle_d2.81512612
X-RAY DIFFRACTIONf_chiral_restr0.052287
X-RAY DIFFRACTIONf_plane_restr0.0052615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6483-1.6670.31193720.3196688X-RAY DIFFRACTION87
1.667-1.68660.33473800.26877653X-RAY DIFFRACTION99
1.6866-1.70720.28463940.25597776X-RAY DIFFRACTION100
1.7072-1.72880.27134180.24217683X-RAY DIFFRACTION100
1.7288-1.75150.26863930.23147656X-RAY DIFFRACTION100
1.7515-1.77550.26634050.22937729X-RAY DIFFRACTION100
1.7755-1.80090.26694010.21747677X-RAY DIFFRACTION100
1.8009-1.82780.24514200.20597730X-RAY DIFFRACTION100
1.8278-1.85630.24254040.20167678X-RAY DIFFRACTION100
1.8563-1.88680.22843940.2067679X-RAY DIFFRACTION100
1.8868-1.91930.24354220.19917770X-RAY DIFFRACTION100
1.9193-1.95420.21633980.1897674X-RAY DIFFRACTION100
1.9542-1.99180.2273730.18857717X-RAY DIFFRACTION100
1.9918-2.03250.21894070.18047717X-RAY DIFFRACTION100
2.0325-2.07660.19044160.17377700X-RAY DIFFRACTION100
2.0766-2.1250.21354450.187650X-RAY DIFFRACTION100
2.125-2.17810.20034220.17047642X-RAY DIFFRACTION100
2.1781-2.2370.20714090.17327715X-RAY DIFFRACTION100
2.237-2.30280.21464200.1757694X-RAY DIFFRACTION99
2.3028-2.37710.2133890.17277705X-RAY DIFFRACTION100
2.3771-2.46210.20574000.17237764X-RAY DIFFRACTION100
2.4621-2.56070.21043740.17977691X-RAY DIFFRACTION99
2.5607-2.67720.20764360.17917637X-RAY DIFFRACTION99
2.6772-2.81830.23283850.17467728X-RAY DIFFRACTION99
2.8183-2.99490.20363760.17617697X-RAY DIFFRACTION99
2.9949-3.22610.19934110.17427675X-RAY DIFFRACTION99
3.2261-3.55060.19394370.16617601X-RAY DIFFRACTION99
3.5506-4.06420.20114050.15627683X-RAY DIFFRACTION98
4.0642-5.11950.18864090.14667628X-RAY DIFFRACTION98
5.1195-48.18880.20134010.18057726X-RAY DIFFRACTION98

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