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

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Basic information

Entry
Database: PDB / ID: 8awp
TitleCrystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant 208 (V19I/R23H/M38I/I60F/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: 1.595 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)26,3302
Polymers26,3302
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-32 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.710, 53.258, 89.490
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: 13165.018 Da / Num. of mol.: 2 / Mutation: V19I, R23H, M38I, I60F, 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.: 152 / 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: 1.89 Å3/Da / Density % sol: 34.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14.2 mg/ml protein concentration 1.6M Sodium citrate tribasic dihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.595→45.77 Å / Num. obs: 27169 / % possible obs: 99.41 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.26 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06499 / Rpim(I) all: 0.02775 / Net I/σ(I): 14.1
Reflection shellResolution: 1.595→1.652 Å / Rmerge(I) obs: 0.7128 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 2590 / CC1/2: 0.837 / CC star: 0.955 / Rpim(I) all: 0.2985 / % possible all: 96.23

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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: 1.595→45.77 Å / SU ML: 0.1448 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8737
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2085 1301 4.8 %
Rwork0.1923 25811 -
obs0.1932 27112 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.58 Å2
Refinement stepCycle: LAST / Resolution: 1.595→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 0 152 1929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731829
X-RAY DIFFRACTIONf_angle_d0.93592469
X-RAY DIFFRACTIONf_chiral_restr0.0656269
X-RAY DIFFRACTIONf_plane_restr0.0086320
X-RAY DIFFRACTIONf_dihedral_angle_d21.4762692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.595-1.660.29111460.25642723X-RAY DIFFRACTION96.5
1.66-1.730.32111600.24942829X-RAY DIFFRACTION99.7
1.73-1.830.26261320.2382835X-RAY DIFFRACTION99.7
1.83-1.940.24421430.20182829X-RAY DIFFRACTION99.7
1.94-2.090.18821460.18332847X-RAY DIFFRACTION99.97
2.09-2.30.19451380.18432881X-RAY DIFFRACTION99.8
2.3-2.630.23271420.19942887X-RAY DIFFRACTION99.8
2.63-3.320.21121420.19822917X-RAY DIFFRACTION99.71
3.32-45.770.17871520.17553063X-RAY DIFFRACTION99.75

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