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- PDB-8zxr: Crystal structure of Ssr1698 in complex with heme c -

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Basic information

Entry
Database: PDB / ID: 8zxr
TitleCrystal structure of Ssr1698 in complex with heme c
Components
  • Cytochrome c
  • Ssr1698 protein
KeywordsMETAL BINDING PROTEIN / Ssr1698 / heme b / heme c
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / apoptotic signaling pathway / mitochondrial intermembrane space / electron transfer activity / lipid binding / heme binding / metal ion binding ...cytochrome c-heme linkage / cytochrome complex / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / apoptotic signaling pathway / mitochondrial intermembrane space / electron transfer activity / lipid binding / heme binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / NICKEL (II) ION / Cytochrome c / Ssr1698 protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
Equus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWang, X. / Liu, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proteins / Year: 2025
Title: Structural Basis for Monomer-Dimer Transition of Dri1 Upon Heme Binding.
Authors: Wang, X.Y. / Zhang, J. / Li, H.Y. / Dong, C.S. / Dai, H.E. / Wang, M. / Liu, L.
History
DepositionJun 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ssr1698 protein
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7307
Polymers12,8902
Non-polymers8405
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-24 kcal/mol
Surface area7340 Å2
MethodPISA
2
A: Ssr1698 protein
B: Cytochrome c
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)82,37942
Polymers77,33812
Non-polymers5,04130
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area28350 Å2
ΔGint-727 kcal/mol
Surface area27120 Å2
MethodPISA
3
A: Ssr1698 protein
B: Cytochrome c
hetero molecules

A: Ssr1698 protein
B: Cytochrome c
hetero molecules

A: Ssr1698 protein
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,18921
Polymers38,6696
Non-polymers2,52115
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area13010 Å2
ΔGint-347 kcal/mol
Surface area14730 Å2
MethodPISA
4
A: Ssr1698 protein
B: Cytochrome c
hetero molecules

A: Ssr1698 protein
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,46014
Polymers25,7794
Non-polymers1,68010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
Buried area4090 Å2
ΔGint-58 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.597, 83.597, 69.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-201-

NI

21A-202-

CL

31A-382-

HOH

41A-383-

HOH

51A-415-

HOH

61B-217-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Ssr1698 protein


Mass: 11643.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: ssr1698 / Production host: Escherichia coli (E. coli) / References: UniProt: P73129
#2: Protein/peptide Cytochrome c


Mass: 1246.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00004

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Non-polymers , 5 types, 144 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Sodium acetate, Sodium formate, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 19377 / % possible obs: 99.9 % / Redundancy: 15.6 % / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.052 / Net I/σ(I): 18.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 15.3 % / Num. unique obs: 1882 / CC1/2: 0.603 / CC star: 0.867 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→36.2 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 967 5 %
Rwork0.1857 --
obs0.1873 19340 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 52 139 987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017878
X-RAY DIFFRACTIONf_angle_d1.2971202
X-RAY DIFFRACTIONf_dihedral_angle_d17.91324
X-RAY DIFFRACTIONf_chiral_restr0.078130
X-RAY DIFFRACTIONf_plane_restr0.011155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.690.30921270.26362550X-RAY DIFFRACTION99
1.69-1.790.31271320.23852565X-RAY DIFFRACTION100
1.79-1.930.21081400.20462591X-RAY DIFFRACTION100
1.93-2.120.2291300.18012594X-RAY DIFFRACTION100
2.12-2.430.20381610.17022589X-RAY DIFFRACTION100
2.43-3.060.19221380.18732660X-RAY DIFFRACTION100
3.06-36.20.21381390.17412824X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -27.1098 Å / Origin y: -23.0813 Å / Origin z: 0.4624 Å
111213212223313233
T0.1473 Å2-0.0034 Å2-0.0137 Å2-0.168 Å20.0051 Å2--0.1728 Å2
L2.4641 °2-0.9084 °2-0.2629 °2-1.606 °2-0.2624 °2--1.7227 °2
S0.0185 Å °-0.0599 Å °0.1484 Å °0.0984 Å °-0.0015 Å °-0.2712 Å °0.011 Å °0.1304 Å °0.0007 Å °
Refinement TLS groupSelection details: all

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