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- PDB-9myp: Structure of Patiria miniata Hop1 chromatin binding region -

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Basic information

Entry
Database: PDB / ID: 9myp
TitleStructure of Patiria miniata 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
NICKEL (II) ION / HORMA domain-containing protein
Similarity search - Component
Biological speciesPatiria miniata (bat star)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 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 Patiria miniata Hop1 chromatin binding region
Authors: Rodriguez, A.A. / Corbett, K.D.
History
DepositionJan 22, 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
C: HORMA domain-containing protein
B: HORMA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,26510
Polymers57,8143
Non-polymers4517
Water5,873326
1
A: HORMA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4614
Polymers19,2711
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HORMA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4023
Polymers19,2711
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: HORMA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4023
Polymers19,2711
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.654, 106.955, 131.402
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: 19271.418 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-terminal MKSSHHHHHHENLYFQSNA tag; methylated lysine (MLY)
Source: (gene. exp.) Patiria miniata (bat star) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A913ZKG6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis Tris pH 6.5, 0.1 M potassium thiocyanate, and 17% 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 / 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: 1.84→82.95 Å / Num. obs: 47903 / % possible obs: 98.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 33.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.7
Reflection shellResolution: 1.84→1.88 Å / Num. unique obs: 2772 / CC1/2: 0.454

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84→82.95 Å / SU ML: 0.2551 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 22.8186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 2424 5.07 %
Rwork0.1979 45401 -
obs0.1997 47825 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.96 Å2
Refinement stepCycle: LAST / Resolution: 1.84→82.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3857 0 7 326 4190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01193941
X-RAY DIFFRACTIONf_angle_d1.12995319
X-RAY DIFFRACTIONf_chiral_restr0.0599577
X-RAY DIFFRACTIONf_plane_restr0.0126690
X-RAY DIFFRACTIONf_dihedral_angle_d15.13151475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.870.3571230.35962500X-RAY DIFFRACTION94.22
1.87-1.920.32491370.3052659X-RAY DIFFRACTION99.43
1.92-1.960.25811410.2672648X-RAY DIFFRACTION99.25
1.96-2.010.28221500.23532629X-RAY DIFFRACTION99.57
2.01-2.060.29551470.23112665X-RAY DIFFRACTION99.68
2.06-2.120.26461460.22772667X-RAY DIFFRACTION99.86
2.12-2.190.24061380.22722676X-RAY DIFFRACTION99.82
2.19-2.270.2541460.23162696X-RAY DIFFRACTION99.54
2.27-2.360.30321500.2192595X-RAY DIFFRACTION98.14
2.36-2.470.27081540.21192665X-RAY DIFFRACTION99.37
2.47-2.60.24561540.20722657X-RAY DIFFRACTION98.18
2.6-2.760.27631360.20962710X-RAY DIFFRACTION99.68
2.76-2.980.25581380.20582714X-RAY DIFFRACTION99.3
2.98-3.280.26181410.19282667X-RAY DIFFRACTION98.6
3.28-3.750.23941260.18252715X-RAY DIFFRACTION98.27
3.75-4.720.17081510.15522670X-RAY DIFFRACTION95.89
4.73-82.950.19891460.18252868X-RAY DIFFRACTION97.6

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