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- PDB-5h7n: Crystal structure of human NLRP12-PYD with a MBP tag -

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Basic information

Entry
Database: PDB / ID: 5h7n
TitleCrystal structure of human NLRP12-PYD with a MBP tag
ComponentsNLRP12-PYD with MBP tag
KeywordsSUGAR BINDING PROTEIN / Maltose binding protein / crystallization tag / death fold
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / 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 / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / 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
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-maltotetraose / DI(HYDROXYETHYL)ETHER / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 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 19, 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _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: NLRP12-PYD with MBP tag
B: NLRP12-PYD with MBP tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,40517
Polymers105,1192
Non-polymers2,28615
Water7,170398
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A: NLRP12-PYD with MBP tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6678
Polymers52,5601
Non-polymers1,1077
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-15 kcal/mol
Surface area19550 Å2
MethodPISA
2
B: NLRP12-PYD with MBP tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7399
Polymers52,5601
Non-polymers1,1798
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-17 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.540, 104.550, 110.940
Angle α, β, γ (deg.)90.00, 98.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein NLRP12-PYD with MBP tag


Mass: 52559.551 Da / Num. of mol.: 2
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-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 411 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 30% PEG 550, 0.2M Ammonium Sulfate, NaAc 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 161270 / % possible obs: 98.6 % / Redundancy: 5.7 % / CC1/2: 0.998 / Net I/σ(I): 17.3
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.636 / % possible all: 96

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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: 1.849→47.182 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.48 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2237 3938 2.48 %
Rwork0.1795 --
obs0.1806 158517 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.849→47.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7113 0 148 398 7659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147454
X-RAY DIFFRACTIONf_angle_d1.3110114
X-RAY DIFFRACTIONf_dihedral_angle_d3.2266066
X-RAY DIFFRACTIONf_chiral_restr0.0811123
X-RAY DIFFRACTIONf_plane_restr0.0091285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8489-1.87140.42711230.38364855X-RAY DIFFRACTION87
1.8714-1.89510.37411330.34585445X-RAY DIFFRACTION98
1.8951-1.920.34221540.32765570X-RAY DIFFRACTION97
1.92-1.94630.38821350.30035486X-RAY DIFFRACTION98
1.9463-1.97410.34211330.2965487X-RAY DIFFRACTION98
1.9741-2.00360.37141420.27245436X-RAY DIFFRACTION98
2.0036-2.03490.28521550.25965600X-RAY DIFFRACTION98
2.0349-2.06830.31331180.24775431X-RAY DIFFRACTION98
2.0683-2.10390.27381420.23345597X-RAY DIFFRACTION98
2.1039-2.14220.24691540.22175502X-RAY DIFFRACTION98
2.1422-2.18340.27711250.22065523X-RAY DIFFRACTION98
2.1834-2.2280.28071430.2135607X-RAY DIFFRACTION99
2.228-2.27640.29461360.21295518X-RAY DIFFRACTION98
2.2764-2.32940.28521430.20615514X-RAY DIFFRACTION98
2.3294-2.38760.27281460.19975556X-RAY DIFFRACTION99
2.3876-2.45220.251350.19275547X-RAY DIFFRACTION99
2.4522-2.52430.25521450.18695588X-RAY DIFFRACTION99
2.5243-2.60580.24741400.18945517X-RAY DIFFRACTION99
2.6058-2.69890.22841390.18155571X-RAY DIFFRACTION98
2.6989-2.8070.26991390.1775579X-RAY DIFFRACTION99
2.807-2.93470.22231400.18715531X-RAY DIFFRACTION99
2.9347-3.08940.20021490.19015545X-RAY DIFFRACTION99
3.0894-3.28290.23981440.18745658X-RAY DIFFRACTION99
3.2829-3.53630.22191490.17785593X-RAY DIFFRACTION99
3.5363-3.8920.18511480.15825587X-RAY DIFFRACTION99
3.892-4.45490.19541360.14115551X-RAY DIFFRACTION99
4.4549-5.61120.17661480.1425582X-RAY DIFFRACTION100
5.6112-47.19730.18171440.15575603X-RAY DIFFRACTION99

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