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

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Basic information

Entry
Database: PDB / ID: 8fjr
TitleStructure of Thermomonospora curvata heme-containing DyP-type peroxidase E293H 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: 1.49 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 E293H 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)88,6074
Polymers87,3742
Non-polymers1,2332
Water13,385743
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-53 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.345, 92.020, 97.466
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: 43687.055 Da / Num. of mol.: 2 / Mutation: E293H
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.: 743 / 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: 1.98 Å3/Da / Density % sol: 38.03 %
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: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 113570 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.99 / Χ2: 0.05 / Net I/σ(I): 11.8 / Num. measured all: 1382610
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Χ2Diffraction-ID% possible all
1.49-1.542.2217440.7390.889199.8
1.54-1.612217360.8361.07199.9
1.61-1.682217370.9211.134199.8
1.68-1.772216920.9531.093199.7
1.77-1.882.1217360.971.041199.8
1.88-2.022.3217470.9841.0641100
2.02-2.232.6217210.9891.104199.9
2.23-2.553217070.991.094199.7
2.55-3.214.3217660.9971.001199.9
3.21-5012.7217010.9920.99199.6

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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: 1.49→39.54 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1764 1936 1.77 %
Rwork0.1513 --
obs0.1517 109176 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 86 743 6409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055820
X-RAY DIFFRACTIONf_angle_d0.8267938
X-RAY DIFFRACTIONf_dihedral_angle_d16.6272156
X-RAY DIFFRACTIONf_chiral_restr0.069826
X-RAY DIFFRACTIONf_plane_restr0.0051066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.530.29151020.2326192X-RAY DIFFRACTION79
1.53-1.570.24261320.20277063X-RAY DIFFRACTION90
1.57-1.620.23531350.18217274X-RAY DIFFRACTION92
1.62-1.670.21991300.16897436X-RAY DIFFRACTION94
1.67-1.730.22361340.16197586X-RAY DIFFRACTION96
1.73-1.80.19151450.15277749X-RAY DIFFRACTION98
1.8-1.880.20651420.15187816X-RAY DIFFRACTION99
1.88-1.980.21061430.14717884X-RAY DIFFRACTION99
1.98-2.10.18561420.14597914X-RAY DIFFRACTION100
2.1-2.260.18321440.14297944X-RAY DIFFRACTION100
2.26-2.490.2041450.14978002X-RAY DIFFRACTION100
2.49-2.850.17571410.15927995X-RAY DIFFRACTION100
2.85-3.590.16291490.15478070X-RAY DIFFRACTION100
3.59-39.540.14951520.14138315X-RAY DIFFRACTION99

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