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- PDB-8awo: Crystal structure of a manganese-containing cupin (tm1459) from T... -

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Basic information

Entry
Database: PDB / ID: 8awo
TitleCrystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant AIFQ (Y7A/M38I/Y83F/C106Q)
ComponentsCupin_2 domain-containing protein
KeywordsMETAL BINDING PROTEIN / cupin / alkene cleavage / amino acid oxidation
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / Cupin type-2 domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGrininger, C. / Steiner, K. / Gruber, K. / Pavkov-Keller, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Research Promotion Agency Austria
CitationJournal: Chem Ing Tech / Year: 2023
Title: Engineering TM1459 for Stabilisation against Inactivation by Amino Acid Oxidation
Authors: Grill, B. / Pavkov-Keller, T. / Grininger, C. / Darnhofer, B. / Gruber, K. / Hall, M. / Schwab, H. / Steiner, K.
History
DepositionAug 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cupin_2 domain-containing protein
B: Cupin_2 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)26,0562
Polymers26,0562
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-33 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.795, 53.733, 90.435
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cupin_2 domain-containing protein


Mass: 13027.924 Da / Num. of mol.: 2 / Mutation: Y7A, M38I, Y83F, C106Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: TM_1459
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9X1H0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 8 mg/ml protein concentration 0.1 M Tris pH 8.5 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→34.6 Å / Num. obs: 23041 / % possible obs: 99.75 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.91 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08215 / Rpim(I) all: 0.03552 / Net I/σ(I): 12.75
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.82 / Num. unique obs: 2219 / CC1/2: 0.836 / CC star: 0.954 / Rpim(I) all: 0.2754

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vj2

1vj2


Resolution: 1.7→34.6 Å / SU ML: 0.2019 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1977
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2416 1155 5.01 %
Rwork0.2088 21883 -
obs0.2105 23038 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.96 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 0 195 1961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451833
X-RAY DIFFRACTIONf_angle_d0.80252476
X-RAY DIFFRACTIONf_chiral_restr0.0598278
X-RAY DIFFRACTIONf_plane_restr0.0065322
X-RAY DIFFRACTIONf_dihedral_angle_d25.5198703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.780.33251370.30472653X-RAY DIFFRACTION98.31
1.78-1.870.28431380.25342687X-RAY DIFFRACTION99.96
1.87-1.990.28171420.22152732X-RAY DIFFRACTION100
1.99-2.140.22231450.21342671X-RAY DIFFRACTION99.96
2.14-2.360.26421540.19882724X-RAY DIFFRACTION100
2.36-2.70.21311380.2142748X-RAY DIFFRACTION100
2.7-3.40.2271440.21552769X-RAY DIFFRACTION99.97
3.4-34.60.23831570.18982899X-RAY DIFFRACTION99.9

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