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- PDB-8fjq: Structure of Thermomonospora curvata heme-containing DyP-type per... -

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Basic information

Entry
Database: PDB / ID: 8fjq
TitleStructure of Thermomonospora curvata heme-containing DyP-type peroxidase E293G mutant
ComponentsDyp-type peroxidase
KeywordsOXIDOREDUCTASE / DyP-type Peroxidase
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dyp-type peroxidase family
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsKhadka, S. / Li, P. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140852 United States
CitationJournal: To Be Published
Title: Structure of Thermomonospora curvata heme-containing DyP-type peroxidase E293G mutant
Authors: Khadka, S. / Geisbrecht, B. / Li, P.
History
DepositionDec 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dyp-type peroxidase
B: Dyp-type peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4454
Polymers87,2122
Non-polymers1,2332
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-55 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.632, 92.405, 97.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dyp-type peroxidase


Mass: 43605.961 Da / Num. of mol.: 2 / Mutation: E293G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Gene: Tcur_2987 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D1A807
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris, pH 6.5, 20% w/v PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 89196 / % possible obs: 99.9 % / Redundancy: 4.1 % / CC1/2: 0.991 / Χ2: 0.047 / Net I/σ(I): 20.3 / Num. measured all: 1101296
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Χ2Diffraction-ID% possible all
1.62-1.683.3170220.6651.071199.4
1.68-1.753170730.8281.093199.9
1.75-1.822.9170790.9221.0631100
1.82-1.923170580.9621.0321100
1.92-2.043.3171010.9781.052199.9
2.04-2.23.1171270.990.9971100
2.2-2.423170630.9930.9981100
2.42-2.773.1170660.9951.0361100
2.77-3.494.6170580.9970.969199.9
3.49-5010.6171030.9961.015199.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5JXU

5jxu


Resolution: 1.62→43.03 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 2004 2.26 %
Rwork0.1723 --
obs0.1729 88843 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5663 0 0 455 6118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065815
X-RAY DIFFRACTIONf_angle_d0.8837930
X-RAY DIFFRACTIONf_dihedral_angle_d14.192156
X-RAY DIFFRACTIONf_chiral_restr0.051825
X-RAY DIFFRACTIONf_plane_restr0.0061066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.31111360.27965842X-RAY DIFFRACTION95
1.66-1.710.27611460.25716168X-RAY DIFFRACTION100
1.71-1.760.26561350.23186164X-RAY DIFFRACTION100
1.76-1.810.23981450.21736159X-RAY DIFFRACTION100
1.81-1.880.24071450.2136134X-RAY DIFFRACTION100
1.88-1.950.23931360.20426189X-RAY DIFFRACTION100
1.95-2.040.21621420.19766209X-RAY DIFFRACTION100
2.04-2.150.21821440.18896191X-RAY DIFFRACTION100
2.15-2.290.20911430.17996193X-RAY DIFFRACTION100
2.29-2.460.18861430.1816211X-RAY DIFFRACTION100
2.46-2.710.22971470.18566242X-RAY DIFFRACTION100
2.71-3.10.19981480.18186282X-RAY DIFFRACTION100
3.1-3.910.19081460.15716314X-RAY DIFFRACTION100
3.91-43.030.16571480.1386541X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -48.5159 Å / Origin y: -7.5983 Å / Origin z: 11.6074 Å
111213212223313233
T0.1845 Å20.0033 Å2-0.0072 Å2-0.1478 Å2-0.0126 Å2--0.1273 Å2
L0.936 °20.1514 °2-0.0322 °2-1.1511 °20.2025 °2--0.8932 °2
S0.0488 Å °0.0088 Å °-0.0157 Å °0.0791 Å °-0.0841 Å °0.0482 Å °-0.1046 Å °-0.0509 Å °0.024 Å °
Refinement TLS groupSelection details: all

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