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

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Basic information

Entry
Database: PDB / ID: 8awn
TitleCrystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant 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: 1.45 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1902
Polymers13,1541
Non-polymers351
Water3,243180
1
A: Cupin_2 domain-containing protein
hetero molecules

A: Cupin_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3794
Polymers26,3082
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3830 Å2
ΔGint-47 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.266, 53.266, 115.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Cupin_2 domain-containing protein


Mass: 13154.059 Da / Num. of mol.: 1 / Mutation: 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1 M LiCl 0.1 M citrate pH 4.0 20 % PEG6000 16 mg/ml protein concentration

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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: Sep 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→37.66 Å / Num. obs: 56128 / % possible obs: 99.89 % / Redundancy: 8.9 % / Biso Wilson estimate: 18.71 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04822 / Rpim(I) all: 0.01703 / Net I/σ(I): 24.33
Reflection shellResolution: 1.45→1.502 Å / Rmerge(I) obs: 0.9108 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 2932 / CC1/2: 0.731 / CC star: 0.919 / Rpim(I) all: 0.3633

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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: 1.45→37.66 Å / SU ML: 0.1308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.7792
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1733 3731 6.65 %
Rwork0.142 52397 -
obs0.1441 56128 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.99 Å2
Refinement stepCycle: LAST / Resolution: 1.45→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 1 180 1082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125949
X-RAY DIFFRACTIONf_angle_d1.17881286
X-RAY DIFFRACTIONf_chiral_restr0.1126142
X-RAY DIFFRACTIONf_plane_restr0.011167
X-RAY DIFFRACTIONf_dihedral_angle_d18.4481371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.3131300.24351882X-RAY DIFFRACTION95.95
1.47-1.490.21871380.22081938X-RAY DIFFRACTION100
1.49-1.510.25551390.21221944X-RAY DIFFRACTION99.95
1.51-1.530.24971330.20471958X-RAY DIFFRACTION100
1.53-1.550.25851400.1821920X-RAY DIFFRACTION100
1.55-1.580.19171390.1811954X-RAY DIFFRACTION100
1.58-1.60.20581360.16391957X-RAY DIFFRACTION100
1.6-1.630.22541420.15221922X-RAY DIFFRACTION100
1.63-1.660.17561370.15041970X-RAY DIFFRACTION100
1.66-1.690.18661370.1411886X-RAY DIFFRACTION100
1.69-1.730.18991430.13371991X-RAY DIFFRACTION100
1.73-1.760.1361400.12271935X-RAY DIFFRACTION99.95
1.76-1.80.17181410.11941933X-RAY DIFFRACTION100
1.8-1.850.17431410.11641940X-RAY DIFFRACTION100
1.85-1.90.13511380.11061938X-RAY DIFFRACTION100
1.9-1.960.15061390.12811940X-RAY DIFFRACTION100
1.96-2.020.13371390.10561967X-RAY DIFFRACTION100
2.02-2.090.15991340.11141931X-RAY DIFFRACTION100
2.09-2.170.14091410.11761921X-RAY DIFFRACTION100
2.18-2.270.14651350.12711964X-RAY DIFFRACTION100
2.27-2.390.16231370.12311930X-RAY DIFFRACTION100
2.39-2.540.16211400.14341964X-RAY DIFFRACTION100
2.54-2.740.19931340.14841916X-RAY DIFFRACTION100
2.74-3.020.14571410.16351968X-RAY DIFFRACTION100
3.02-3.450.18321380.15171942X-RAY DIFFRACTION100
3.45-4.350.17191400.13791940X-RAY DIFFRACTION100
4.35-37.660.1931390.15171946X-RAY DIFFRACTION99.9

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