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- PDB-8fm6: Dri1 hemoprotein variant H21A with a zinc-mirror heme site -

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Basic information

Entry
Database: PDB / ID: 8fm6
TitleDri1 hemoprotein variant H21A 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 / metal ion binding / HEME B/C / Ssr1698 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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
DepositionDec 22, 2022Deposition 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
A: Ssr1698 protein
B: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0983
Polymers22,4792
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, The Rg value and calculated P(r) distribution curve support a dimeric species formed in the presence of bound heme.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-20 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.659, 74.659, 211.188
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 2 through 95)
d_2ens_1(chain "B" and resid 2 through 95)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAASNA1 - 94
d_21ens_1ALAASNB1 - 94

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Components

#1: Protein Ssr1698 protein


Mass: 11239.646 Da / Num. of mol.: 2 / Mutation: H21A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / 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.: 1 / 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: 3.78 Å3/Da / Density % sol: 67.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium citrate, 0.1 M potassium phosphate, 34% PEG8000

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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: Oct 16, 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: 2.85→36.76 Å / Num. obs: 8771 / % possible obs: 81.64 % / Redundancy: 10 % / Biso Wilson estimate: 81.6 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.049 / Rrim(I) all: 0.156 / Net I/σ(I): 10.7
Reflection shellResolution: 2.851→3.05 Å / Redundancy: 12.8 % / Rmerge(I) obs: 2.395 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 106 / CC1/2: 0.436 / Rpim(I) all: 0.691 / Rrim(I) all: 2.495 / % possible all: 63.7

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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: 2.85→36.76 Å / SU ML: 0.3329 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.271 353 4.92 %
Rwork0.2193 6816 -
obs0.2216 7169 81.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.57 Å2
Refinement stepCycle: LAST / Resolution: 2.85→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 43 0 1523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721548
X-RAY DIFFRACTIONf_angle_d0.94772105
X-RAY DIFFRACTIONf_chiral_restr0.0551233
X-RAY DIFFRACTIONf_plane_restr0.0063275
X-RAY DIFFRACTIONf_dihedral_angle_d15.1106575
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.921678426611 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.050.3673680.30251156X-RAY DIFFRACTION43.37
3.26-4.110.28651450.24392722X-RAY DIFFRACTION99.97
4.11-36.760.24841400.19952938X-RAY DIFFRACTION99.81
Refinement TLS params.Method: refined / Origin x: -26.9976013583 Å / Origin y: 19.4440202137 Å / Origin z: -1.77762991529 Å
111213212223313233
T0.489453433326 Å2-0.000561693296934 Å2-0.100022798936 Å2-0.301019570875 Å2-0.0460128096031 Å2--0.49356933024 Å2
L2.62001280465 °21.23926636007 °22.23804984715 °2-0.694272354492 °20.625109540459 °2--3.23057436902 °2
S0.307976843423 Å °-0.0916863761381 Å °-0.0696665904682 Å °0.538951047203 Å °-0.133350014788 Å °-0.320456762704 Å °0.395650697533 Å °-0.0673027943853 Å °-0.128145732652 Å °
Refinement TLS groupSelection details: all

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