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- PDB-9mug: Structure of Schistosoma mansoni Hop1 chromatin binding region -

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Basic information

Entry
Database: PDB / ID: 9mug
TitleStructure of Schistosoma mansoni Hop1 chromatin binding region
ComponentsHORMA domain-containing protein
KeywordsDNA BINDING PROTEIN / Meiosis / PHD domain / winged-helix domain
Function / homology
Function and homology information


meiotic cell cycle / chromosome / zinc ion binding / nucleus
Similarity search - Function
: / PhD finger domain / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
HORMA domain-containing protein
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsRodriguez, A.R. / Ye, Q. / Nguyen, J. / Chau, K. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM144121 United States
CitationJournal: To Be Published
Title: Structure of Schistosoma mansoni Hop1 chromatin binding region
Authors: Rodriguez, A.A. / Corbett, K.D.
History
DepositionJan 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HORMA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4313
Polymers17,3001
Non-polymers1312
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.032, 64.959, 65.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein HORMA domain-containing protein


Mass: 17299.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q0KSN1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 0.1 M sodium acetate, and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2827 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 1.45→64.96 Å / Num. obs: 135024 / % possible obs: 94.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 13.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.9
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.458 / Num. unique obs: 605 / CC1/2: 0.557

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→32.63 Å / SU ML: 0.1206 / Cross valid method: FREE R-VALUE / σ(F): 0.45 / Phase error: 16.5095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1583 1157 4.81 %
Rwork0.1288 22884 -
obs0.1303 24041 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.26 Å2
Refinement stepCycle: LAST / Resolution: 1.45→32.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 2 216 1400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421201
X-RAY DIFFRACTIONf_angle_d1.38211620
X-RAY DIFFRACTIONf_chiral_restr0.0816183
X-RAY DIFFRACTIONf_plane_restr0.0096212
X-RAY DIFFRACTIONf_dihedral_angle_d20.2545457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.520.23161170.16521965X-RAY DIFFRACTION66.24
1.52-1.60.16051140.1142769X-RAY DIFFRACTION91.52
1.6-1.70.17341570.0982900X-RAY DIFFRACTION96.89
1.7-1.830.14231460.10282971X-RAY DIFFRACTION98.51
1.83-2.010.17221280.10473021X-RAY DIFFRACTION99.31
2.01-2.30.14191640.11023025X-RAY DIFFRACTION99.56
2.3-2.90.14821630.13673079X-RAY DIFFRACTION99.82
2.9-32.630.16181680.14953154X-RAY DIFFRACTION97.88

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