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- PDB-3wur: Structure of DMP19 Complex with 18-crown-6 -

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Basic information

Entry
Database: PDB / ID: 3wur
TitleStructure of DMP19 Complex with 18-crown-6
ComponentsUncharacterized protein
KeywordsGENE REGULATION / helix bundle / DNA mimic
Function / homologyA middle domain of Talin 1 - #60 / Domain of unknown function DUF4375 / DMP19-like protein / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / L(+)-TARTARIC ACID / DNA mimic protein DMP19
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsLee, C.C. / Wang, H.C. / Wang, A.H.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Crowning proteins: modulating the protein surface properties using crown ethers.
Authors: Lee, C.C. / Maestre-Reyna, M. / Hsu, K.C. / Wang, H.C. / Liu, C.I. / Jeng, W.Y. / Lin, L.L. / Wood, R. / Chou, C.C. / Yang, J.M. / Wang, A.H.
History
DepositionMay 2, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,76713
Polymers38,7152
Non-polymers2,05211
Water8,791488
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0445
Polymers19,3571
Non-polymers6874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7238
Polymers19,3571
Non-polymers1,3657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.100, 67.100, 176.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 19357.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0541 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K0P4

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Non-polymers , 5 types, 499 molecules

#2: Chemical
ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H24O6
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 0.2M Potassium sodium tartrate, 0.1M Na citrate, 1.6M Ammonium sulfate , pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 71243 / % possible obs: 98 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 58.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→29.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.894 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3570 5 %RANDOM
Rwork0.169 ---
obs0.17 67437 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0 Å20 Å2
2--0.32 Å2-0 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 136 488 3218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.022787
X-RAY DIFFRACTIONr_bond_other_d0.0070.0212586
X-RAY DIFFRACTIONr_angle_refined_deg3.0251.9963747
X-RAY DIFFRACTIONr_angle_other_deg2.233.0446002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5435325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50225.224134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9391510
X-RAY DIFFRACTIONr_chiral_restr0.2820.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213051
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02603
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7351.6061306
X-RAY DIFFRACTIONr_mcbond_other1.7221.6031305
X-RAY DIFFRACTIONr_mcangle_it2.4222.4031629
X-RAY DIFFRACTIONr_mcangle_other2.4222.4071630
X-RAY DIFFRACTIONr_scbond_it3.5692.0161479
X-RAY DIFFRACTIONr_scbond_other3.5712.0151476
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.12.8852114
X-RAY DIFFRACTIONr_long_range_B_refined7.04516.3523759
X-RAY DIFFRACTIONr_long_range_B_other7.04616.3493758
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 234 -
Rwork0.232 4961 -
obs--97.98 %

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