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- PDB-8gf4: Crystal structure of Domain Related to Iron (DRI) in complex with heme -

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Basic information

Entry
Database: PDB / ID: 8gf4
TitleCrystal structure of Domain Related to Iron (DRI) in complex with heme
ComponentsSsr1698 protein
KeywordsMETAL BINDING PROTEIN / Heme binding protein / DRI-Heme complex / DUF2470 domain / Iron homeostasis
Function / homologyDomain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Ssr1698 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKumaran, D. / Blaby, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)Quantitative Plant Science Initiative, SFA United States
CitationJournal: Nat Commun / Year: 2024
Title: A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria.
Authors: Grosjean, N. / Yee, E.F. / Kumaran, D. / Chopra, K. / Abernathy, M. / Biswas, S. / Byrnes, J. / Kreitler, D.F. / Cheng, J.F. / Ghosh, A. / Almo, S.C. / Iwai, M. / Niyogi, K.K. / Pakrasi, H.B. ...Authors: Grosjean, N. / Yee, E.F. / Kumaran, D. / Chopra, K. / Abernathy, M. / Biswas, S. / Byrnes, J. / Kreitler, D.F. / Cheng, J.F. / Ghosh, A. / Almo, S.C. / Iwai, M. / Niyogi, K.K. / Pakrasi, H.B. / Sarangi, R. / van Dam, H. / Yang, L. / Blaby, I.K. / Blaby-Haas, C.E.
History
DepositionMar 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ssr1698 protein
B: Ssr1698 protein
C: Ssr1698 protein
D: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,72110
Polymers45,2274
Non-polymers1,4956
Water543
1
A: Ssr1698 protein
B: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3615
Polymers22,6132
Non-polymers7473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-102 kcal/mol
Surface area9450 Å2
MethodPISA
2
C: Ssr1698 protein
D: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3615
Polymers22,6132
Non-polymers7473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-101 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.976, 42.976, 379.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Ssr1698 protein / Domain Related to Iron / DRI


Mass: 11306.716 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: ssr1698 / Production host: Escherichia coli (E. coli) / References: UniProt: P73129
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 23% PEG3350, 100 mM Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2019
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7898 / % possible obs: 92.6 % / Redundancy: 3.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.092 / Net I/σ(I): 6
Reflection shellResolution: 3→3.08 Å / Rmerge(I) obs: 0.504 / Num. unique obs: 830 / CC1/2: 0.969

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Processing

Software
NameVersionClassification
ADSCdata collection
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→37.25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.848 / SU B: 25.065 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.605 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27914 763 10.4 %RANDOM
Rwork0.20122 ---
obs0.20602 6550 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.834 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å21.29 Å2-0 Å2
2--2.58 Å2-0 Å2
3----8.36 Å2
Refinement stepCycle: 1 / Resolution: 3→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 90 3 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132860
X-RAY DIFFRACTIONr_bond_other_d0.0050.0152692
X-RAY DIFFRACTIONr_angle_refined_deg2.081.6973888
X-RAY DIFFRACTIONr_angle_other_deg1.2271.616216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8885356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.48124.706136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.69715496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1171512
X-RAY DIFFRACTIONr_chiral_restr0.0580.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023274
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02588
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_it5.5667.011436
X-RAY DIFFRACTIONr_mcbond_other5.5697.011434
X-RAY DIFFRACTIONr_mcangle_it8.75810.5061788
X-RAY DIFFRACTIONr_mcangle_other8.75910.5051788
X-RAY DIFFRACTIONr_scbond_it5.377.041424
X-RAY DIFFRACTIONr_scbond_other5.3687.041425
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.22810.4012101
X-RAY DIFFRACTIONr_long_range_B_refined12.10680.7473178
X-RAY DIFFRACTIONr_long_range_B_other12.10880.7123176
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 67 -
Rwork0.253 535 -
obs--99.01 %

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