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- PDB-5wpz: Crystal structure of MNDA PYD with MBP tag -

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Basic information

Entry
Database: PDB / ID: 5wpz
TitleCrystal structure of MNDA PYD with MBP tag
ComponentsMBP-hMNDA-PYD
KeywordsSUGAR BINDING PROTEIN / death fold / MBP tag / crystallization tag
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 / periplasmic space / DNA damage response / membrane
Similarity search - Function
Death Domain, Fas / Death Domain, Fas / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 22, 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

Downloads & links

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Assembly

Deposited unit
A: MBP-hMNDA-PYD
B: MBP-hMNDA-PYD
C: MBP-hMNDA-PYD
D: MBP-hMNDA-PYD
E: MBP-hMNDA-PYD
F: MBP-hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,88012
Polymers316,8266
Non-polymers2,0546
Water20,5731142
1
A: MBP-hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1472
Polymers52,8041
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MBP-hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1472
Polymers52,8041
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MBP-hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1472
Polymers52,8041
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MBP-hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1472
Polymers52,8041
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: MBP-hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1472
Polymers52,8041
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: MBP-hMNDA-PYD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1472
Polymers52,8041
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)192.150, 235.610, 73.760
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
MBP-hMNDA-PYD


Mass: 52804.348 Da / Num. of mol.: 6
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.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1142 / 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: 2.63 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 15% PEG 4000, 0.2M NH4Ac, 0.1M NaAc, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 201859 / % possible obs: 89 % / Redundancy: 13.6 % / CC1/2: 0.999 / Net I/σ(I): 20.4
Reflection shellResolution: 2→2.12 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 3.4 / CC1/2: 0.937 / % possible all: 53.4

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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: 2→48.361 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.88
RfactorNum. reflection% reflection
Rfree0.2688 10003 4.96 %
Rwork0.2206 --
obs0.223 201675 88.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→48.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21442 0 138 1142 22722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322138
X-RAY DIFFRACTIONf_angle_d0.5730011
X-RAY DIFFRACTIONf_dihedral_angle_d2.20217629
X-RAY DIFFRACTIONf_chiral_restr0.043349
X-RAY DIFFRACTIONf_plane_restr0.0043831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9981-2.02080.38781840.31513159X-RAY DIFFRACTION45
2.0208-2.04450.3582060.28853557X-RAY DIFFRACTION50
2.0445-2.06950.35581900.28963832X-RAY DIFFRACTION54
2.0695-2.09570.37852110.30134115X-RAY DIFFRACTION58
2.0957-2.12320.32832220.29294472X-RAY DIFFRACTION63
2.1232-2.15230.36482600.28254731X-RAY DIFFRACTION67
2.1523-2.18310.31712600.27375240X-RAY DIFFRACTION73
2.1831-2.21570.32462860.25995742X-RAY DIFFRACTION81
2.2157-2.25030.33993230.2686601X-RAY DIFFRACTION92
2.2503-2.28720.31493560.26997099X-RAY DIFFRACTION99
2.2872-2.32660.32373620.25536968X-RAY DIFFRACTION98
2.3266-2.36890.31033890.25257026X-RAY DIFFRACTION99
2.3689-2.41450.30223580.25327040X-RAY DIFFRACTION99
2.4145-2.46380.30813810.25257049X-RAY DIFFRACTION98
2.4638-2.51730.30163260.25567132X-RAY DIFFRACTION100
2.5173-2.57590.2983740.25947033X-RAY DIFFRACTION98
2.5759-2.64030.31233910.26217092X-RAY DIFFRACTION99
2.6403-2.71170.32623750.25567097X-RAY DIFFRACTION100
2.7117-2.79150.31973670.26077079X-RAY DIFFRACTION99
2.7915-2.88160.29073530.26527103X-RAY DIFFRACTION99
2.8816-2.98450.30943830.26227151X-RAY DIFFRACTION99
2.9845-3.1040.29283550.24487163X-RAY DIFFRACTION99
3.104-3.24520.31093840.24557117X-RAY DIFFRACTION99
3.2452-3.41630.29314040.23297150X-RAY DIFFRACTION100
3.4163-3.63030.27624350.2137152X-RAY DIFFRACTION100
3.6303-3.91050.24833320.19957268X-RAY DIFFRACTION100
3.9105-4.30380.21263710.17737250X-RAY DIFFRACTION100
4.3038-4.9260.21123710.15357302X-RAY DIFFRACTION100
4.926-6.20420.19833980.17267354X-RAY DIFFRACTION100
6.2042-48.37560.18153960.1597598X-RAY DIFFRACTION99

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