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- PDB-9gt0: DTPAA CHIP EXPERIMENT, ID29, X,Y SPACING 100,100 -

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Basic information

Entry
Database: PDB / ID: 9gt0
TitleDTPAA CHIP EXPERIMENT, ID29, X,Y SPACING 100,100
ComponentsDeferrochelatase
KeywordsOXIDOREDUCTASE / PEROXIDASE / RADIATION DAMAGE / SERIAL CRYSTALLOGRAPHY
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 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsGorel, A. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Iucrj / Year: 2025
Title: Testing the limits: serial crystallography using unpatterned fixed targets.
Authors: Gorel, A. / Shoeman, R.L. / Hartmann, E. / Nizinski, S. / Appleby, M.V. / Beale, E.V. / Dworkowski, F. / Gotthard, G.C. / Beale, J.H. / Holton, J. / Doak, R.B. / Barends, T.R.M. / Schlichting, I.
History
DepositionSep 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)79,8914
Polymers78,6582
Non-polymers1,2332
Water10,773598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.600, 68.800, 75.500
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deferrochelatase / Peroxidase EfeB


Mass: 39329.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SLI_2602 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A7U9DT46, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#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.: 598 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: batch mode / Details: PEG 6K, HEPES pH 7.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.073 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Jan 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.073 Å / Relative weight: 1
ReflectionResolution: 1.67→40 Å / Num. obs: 84225 / % possible obs: 100 % / Redundancy: 700 % / R split: 0.122 / Net I/σ(I): 7
Reflection shellResolution: 1.67→1.71 Å / Num. unique obs: 4221 / R split: 1.14

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystFELdata scaling
CrystFELdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→37.66 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.227 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17157 4325 5.1 %RANDOM
Rwork0.1461 ---
obs0.14748 79872 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0.24 Å2
2---0.54 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.67→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5539 0 86 598 6223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135882
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175389
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.6768033
X-RAY DIFFRACTIONr_angle_other_deg1.4231.59812419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6145752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6320.326337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55615884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3341561
X-RAY DIFFRACTIONr_chiral_restr0.0830.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026863
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021404
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_it1.9172.2552940
X-RAY DIFFRACTIONr_mcbond_other1.892.2542938
X-RAY DIFFRACTIONr_mcangle_it2.6473.3723681
X-RAY DIFFRACTIONr_mcangle_other2.6333.3713681
X-RAY DIFFRACTIONr_scbond_it3.1952.6152942
X-RAY DIFFRACTIONr_scbond_other3.1962.6152940
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0133.7634340
X-RAY DIFFRACTIONr_long_range_B_refined9.31926.896335
X-RAY DIFFRACTIONr_long_range_B_other8.9726.5856265
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 324 -
Rwork0.384 5874 -
obs--99.81 %

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