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- PDB-8zxq: Crystal structure of Ssr1698 in complex with heme b -

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Basic information

Entry
Database: PDB / ID: 8zxq
TitleCrystal structure of Ssr1698 in complex with heme b
ComponentsSsr1698 protein
KeywordsMETAL BINDING PROTEIN / Ssr1698 / heme b / heme c
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. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2602
Polymers11,6431
Non-polymers6161
Water91951
1
A: Ssr1698 protein
hetero molecules

A: Ssr1698 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5194
Polymers23,2862
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3110 Å2
ΔGint-44 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.898, 92.348, 34.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-200-

HEM

21A-306-

HOH

31A-346-

HOH

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Components

#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: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: HEPES, Sodium citrate tribasic dihydrate

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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: Nov 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 14985 / % possible obs: 99.8 % / Redundancy: 12.3 % / CC1/2: 0.994 / CC star: 0.999 / Net I/σ(I): 50.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.353 / Num. unique obs: 1485 / CC1/2: 0.875 / CC star: 0.966 / Rpim(I) all: 0.393 / % possible all: 99.7

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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: 1.51→27.28 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 721 5.19 %
Rwork0.1745 --
obs0.1763 13896 92.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 43 51 801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009794
X-RAY DIFFRACTIONf_angle_d0.9861092
X-RAY DIFFRACTIONf_dihedral_angle_d16.488295
X-RAY DIFFRACTIONf_chiral_restr0.049117
X-RAY DIFFRACTIONf_plane_restr0.007141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.630.25571030.24571705X-RAY DIFFRACTION61
1.63-1.790.23991530.20452810X-RAY DIFFRACTION100
1.79-2.050.22021530.16952833X-RAY DIFFRACTION100
2.05-2.590.21741550.16062858X-RAY DIFFRACTION100
2.59-27.280.18551570.16372969X-RAY DIFFRACTION99

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