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- PDB-9epd: DtpAa Y389F 8 fs 10 microjoules XFEL Pulse Data Collection -

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Basic information

Entry
Database: PDB / ID: 9epd
TitleDtpAa Y389F 8 fs 10 microjoules XFEL Pulse Data Collection
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / peroxidase / heme
Function / homology
Function and homology information


iron import into cell / cell envelope / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / lyase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
Deferrochelatase / : / : / 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
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Deferrochelatase
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsWilliams, L.J. / Owen, R.L. / Worrall, J.A.R. / Hough, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light SourceSTU0436 United Kingdom
CitationJournal: To Be Published
Title: DtpAa Y389F 8 fs 10 microjoules XFEL Pulse Data Collection
Authors: Williams, L.J. / Owen, R.L. / Worrall, J.A.R. / Hough, M.A.
History
DepositionMar 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deferrochelatase
B: Deferrochelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7134
Polymers80,4802
Non-polymers1,2332
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-63 kcal/mol
Surface area27010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.720, 68.200, 74.600
Angle α, β, γ (deg.)90.00, 105.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deferrochelatase


Mass: 40240.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: SLI_2602 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A7U9DT46
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 298 K / Method: batch mode / Details: 12% v/v PEG 3350, 100 mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 294.15 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.03 Å
DetectorType: PSI JUNGFRAU 8M / Detector: PIXEL / Date: Sep 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.44→35.05 Å / Num. obs: 129619 / % possible obs: 100 % / Redundancy: 71.3 % / CC1/2: 0.888 / Net I/σ(I): 3.23
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 47.7 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 6442 / CC1/2: 0.336 / % possible all: 100
Serial crystallography measurementPulse duration: 9 fsec. / Pulse energy: 100 µJ / Pulse photon energy: 12.03 keV / Source distance: 0.111 m
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Cootmodel building
CrystFELdata scaling
REFMACphasing
CrystFELdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→35.05 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.994 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20476 5899 5 %RANDOM
Rwork0.17742 ---
obs0.1788 111068 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0 Å20.54 Å2
2--0.23 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.48→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 86 533 6163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125829
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165428
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.857940
X-RAY DIFFRACTIONr_angle_other_deg0.6551.78912433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.541564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51910881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027248
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021482
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8421.5332906
X-RAY DIFFRACTIONr_mcbond_other4.8261.5322905
X-RAY DIFFRACTIONr_mcangle_it6.842.763632
X-RAY DIFFRACTIONr_mcangle_other6.8422.7613633
X-RAY DIFFRACTIONr_scbond_it6.211.8062923
X-RAY DIFFRACTIONr_scbond_other6.2111.8062921
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9713.1694302
X-RAY DIFFRACTIONr_long_range_B_refined13.62116.526482
X-RAY DIFFRACTIONr_long_range_B_other13.13716.26436
X-RAY DIFFRACTIONr_rigid_bond_restr3.901311257
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 428 -
Rwork0.284 8183 -
obs--99.9 %

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