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- PDB-8gbk: Dri1 hemoprotein variant H79A-R90A with a zinc-mirror heme site -

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Basic information

Entry
Database: PDB / ID: 8gbk
TitleDri1 hemoprotein variant H79A-R90A with a zinc-mirror heme site
ComponentsSsr1698 protein
KeywordsMETAL BINDING PROTEIN / heme / DRI domain
Function / homologyDomain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / HEME B/C / Ssr1698 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYee, E.F. / Blaby-Haas, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionFeb 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Ssr1698 protein
H: Ssr1698 protein
B: Ssr1698 protein
E: Ssr1698 protein
A: Ssr1698 protein
C: Ssr1698 protein
D: Ssr1698 protein
F: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,70212
Polymers89,2288
Non-polymers2,4744
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, SAXS experiments confirm the protein is dimeric when bound to heme
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Ssr1698 protein
B: Ssr1698 protein
E: Ssr1698 protein
A: Ssr1698 protein
C: Ssr1698 protein
D: Ssr1698 protein
F: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,54911
Polymers78,0757
Non-polymers2,4744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: Ssr1698 protein
B: Ssr1698 protein
E: Ssr1698 protein
A: Ssr1698 protein
C: Ssr1698 protein
D: Ssr1698 protein
F: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,54911
Polymers78,0757
Non-polymers2,4744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: Ssr1698 protein
B: Ssr1698 protein
E: Ssr1698 protein
A: Ssr1698 protein
C: Ssr1698 protein
D: Ssr1698 protein
F: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,54911
Polymers78,0757
Non-polymers2,4744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.815, 91.815, 144.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 3 through 94)
d_2ens_1(chain "B" and resid 3 through 94)
d_3ens_1(chain "C" and resid 3 through 94)
d_4ens_1(chain "D" and resid 3 through 94)
d_5ens_1(chain "E" and resid 3 through 94)
d_6ens_1(chain "F" and resid 3 through 94)
d_7ens_1(chain "G" and resid 3 through 94)
d_8ens_1(chain "H" and resid 3 through 94)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 3 - 94 / Label seq-ID: 3 - 94

Dom-IDAuth asym-IDLabel asym-ID
d_1AE
d_2BC
d_3CF
d_4DG
d_5ED
d_6FH
d_7GA
d_8HB

NCS oper:
IDCodeMatrixVector
1given(0.99693687864, 0.0756615441926, -0.0198038061659), (0.0759749825435, -0.996987940266, 0.0155836129254), (-0.0185650757007, -0.0170404722555, -0.999682429709)1.72023095954, 0.0257098708211, 51.7513792793
2given(-0.122734144524, 0.990243504775, -0.0659858395366), (0.991245352424, 0.119054400137, -0.0570850339856), (-0.0486721795805, -0.0724144395778, -0.996186311829)0.666735747047, 3.95729885463, 71.9850848022
3given(-0.999831784133, 0.00584827860193, 0.0173839315401), (0.00644877405442, 0.999377307226, 0.0346902164109), (-0.0171702286412, 0.0347964860127, -0.999246910333)-46.3240331197, 45.017032517, 24.0262333515
4given(-0.0409268291588, 0.998369520096, -0.0397906521349), (-0.999065788375, -0.0403373544534, 0.0155063965641), (0.013876064057, 0.0403881068882, 0.999087711699)0.701605380108, -1.46930964835, -20.8179493857
5given(0.116035351257, -0.989986723939, 0.0803870865474), (0.992398698855, 0.112215666215, -0.0505219434151), (0.0409953627766, 0.0856383715448, 0.995482520967)-47.0164566785, 49.4844157899, -48.142984524
6given(-0.998228568552, -0.0528052895292, 0.0274103324298), (-0.0536029260572, 0.998134437001, -0.0292296423399), (-0.0258157170013, -0.0306471380547, -0.9991968283)-48.1262637176, 46.1328404812, 80.4793245122
7given(0.0652345513799, -0.99765612863, 0.0206567740268), (0.997710700885, 0.0648403363373, -0.0192116663153), (0.0178272444651, 0.0218627489257, 0.99960202559)-46.1727460066, 47.2499143143, 7.93983903576

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Components

#1: Protein
Ssr1698 protein


Mass: 11153.530 Da / Num. of mol.: 8 / Mutation: H79A,R90A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / Gene: ssr1698 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P73129
#2: Chemical
ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
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: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, 0.2 M sodium chloride, 0.75-1.5 M ammonium sulfate
PH range: 4.6 - 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-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 23, 2022 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.9→29.94 Å / Num. obs: 26403 / % possible obs: 93.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 70.5 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.079 / Rrim(I) all: 0.157 / Net I/σ(I): 5.6
Reflection shellResolution: 2.9→3.02 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.972 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2612 / CC1/2: 0.689 / CC star: 0.823 / Rpim(I) all: 0.57 / Rrim(I) all: 1.13 / % possible all: 48.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC1.0.5data processing
Aimless0.7.7data scaling
XDSJan 10, 2022data reduction
PHASER2.8.3phasing
Coot0.9.5model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.94 Å / Cross valid method: FREE R-VALUE / σ(F): 2.18 / Phase error: 38.5422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3257 1978 7.57 %
Rwork0.3109 24164 -
obs0.3097 26142 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5748 0 172 0 5920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00896014
X-RAY DIFFRACTIONf_angle_d1.23028186
X-RAY DIFFRACTIONf_chiral_restr0.0774917
X-RAY DIFFRACTIONf_plane_restr0.00491068
X-RAY DIFFRACTIONf_dihedral_angle_d15.96382221
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EAX-RAY DIFFRACTIONTorsion NCS1.46833371481
ens_1d_3EAX-RAY DIFFRACTIONTorsion NCS1.66628302033
ens_1d_4EAX-RAY DIFFRACTIONTorsion NCS1.92176397125
ens_1d_5EAX-RAY DIFFRACTIONTorsion NCS0.762132816182
ens_1d_6EAX-RAY DIFFRACTIONTorsion NCS1.25438709843
ens_1d_7EAX-RAY DIFFRACTIONTorsion NCS1.25646364434
ens_1d_8EAX-RAY DIFFRACTIONTorsion NCS1.01065489669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.3681430.361722X-RAY DIFFRACTION92.09
2.97-3.050.35241380.34921754X-RAY DIFFRACTION91.98
3.05-3.140.3851360.35361711X-RAY DIFFRACTION92.14
3.14-3.240.37121470.35211747X-RAY DIFFRACTION92.09
3.24-3.360.35931380.34441721X-RAY DIFFRACTION92.03
3.36-3.490.31111440.35221741X-RAY DIFFRACTION91.82
3.49-3.650.33731460.3231733X-RAY DIFFRACTION91.26
3.65-3.840.37231400.32441723X-RAY DIFFRACTION91.84
3.85-4.090.32231350.30291727X-RAY DIFFRACTION91.91
4.09-4.40.28531420.26711760X-RAY DIFFRACTION91.91
4.4-4.840.2921460.26411729X-RAY DIFFRACTION91.34
4.84-5.540.26781400.27561737X-RAY DIFFRACTION91.61
5.54-6.960.35531410.32831741X-RAY DIFFRACTION91.82
6.96-29.940.30741370.30051623X-RAY DIFFRACTION84.05
Refinement TLS params.Method: refined / Origin x: -23.2768715797 Å / Origin y: 15.5767452014 Å / Origin z: 14.348531701 Å
111213212223313233
T0.506322985179 Å20.0607772729898 Å20.0109436152253 Å2-0.563568057438 Å20.0323143204948 Å2--0.455458245658 Å2
L0.178433243407 °20.0320919518054 °2-0.214934146041 °2-0.132802513051 °20.0616585209296 °2--0.799191707735 °2
S0.120648435443 Å °0.0798954662615 Å °-0.00779281325749 Å °-0.0619198136032 Å °0.0849075603188 Å °0.0530010689296 Å °-0.0941583280787 Å °-0.20957264792 Å °-0.204585160878 Å °
Refinement TLS groupSelection details: all

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