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- PDB-7bp2: Structural mechanism directing nucleosome reorganization by NAP1-... -

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Basic information

Entry
Database: PDB / ID: 7bp2
TitleStructural mechanism directing nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)
Components
  • Histone H2A.6
  • Histone H2B.1
KeywordsNUCLEAR PROTEIN / complex / Histone / PLANT PROTEIN
Function / homology
Function and homology information


DNA-mediated transformation / plastid / chloroplast / response to bacterium / response to wounding / structural constituent of chromatin / nucleosome / protein heterodimerization activity / nucleolus / DNA binding ...DNA-mediated transformation / plastid / chloroplast / response to bacterium / response to wounding / structural constituent of chromatin / nucleosome / protein heterodimerization activity / nucleolus / DNA binding / extracellular region / nucleus
Similarity search - Function
Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 ...Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2A.6 / Histone H2B.1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLuo, Q. / Baihui, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: NAP1-Related Protein 1 (NRP1) has multiple interaction modes for chaperoning histones H2A-H2B.
Authors: Luo, Q. / Wang, B. / Wu, Z. / Jiang, W. / Wang, Y. / Du, K. / Zhou, N. / Zheng, L. / Gan, J. / Shen, W.H. / Ma, J. / Dong, A.
History
DepositionMar 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H2A.6
B: Histone H2B.1
C: Histone H2A.6
D: Histone H2B.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,46418
Polymers42,1354
Non-polymers1,32914
Water7,062392
1
A: Histone H2A.6
B: Histone H2B.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7329
Polymers21,0682
Non-polymers6657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-110 kcal/mol
Surface area9270 Å2
MethodPISA
2
C: Histone H2A.6
D: Histone H2B.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7329
Polymers21,0682
Non-polymers6657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-105 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.712, 65.712, 96.687
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Histone H2A.6 / HTA1 / Protein RESISTANT TO AGROBACTERIUM TRANSFORMATION 5


Mass: 10033.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RAT5, H2A-1, At5g54640, MRB17.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LD28
#2: Protein Histone H2B.1 / HTB1


Mass: 11033.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g07790, F24B9.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LQQ4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium sulphate 0.1M Bis Tris propane pH 7.5 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.514
11K, H, -L20.486
ReflectionResolution: 1.58→30 Å / Num. obs: 64079 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.016 / Rrim(I) all: 0.052 / Χ2: 0.949 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.647.10.29963480.9320.1160.3210.86199.9
1.64-1.77.50.25564570.9630.0960.2730.90499.9
1.7-1.787.80.19964150.9790.0730.2120.9699.9
1.78-1.878.10.14863960.990.0530.1581.03699.8
1.87-1.998.90.11464320.9940.0390.1211.109100
1.99-2.1490.08563490.9960.0290.0891.168100
2.14-2.368.90.06664310.9970.0230.071.11699.9
2.36-2.79.90.05564060.9980.0180.0580.933100
2.7-3.410.10.04364090.9990.0140.0460.79100
3.4-3010.20.03764360.9990.0120.0390.662100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOI

1aoi


Resolution: 1.58→28.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.936 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.013 / ESU R Free: 0.015
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 3127 4.9 %RANDOM
Rwork0.1549 ---
obs0.1564 60749 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.81 Å2 / Biso mean: 16.962 Å2 / Biso min: 3.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å2-0 Å2
2---0.32 Å2-0 Å2
3---0.65 Å2
Refinement stepCycle: final / Resolution: 1.58→28.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 74 392 3188
Biso mean--38.03 31.47 -
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132820
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172797
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.6433794
X-RAY DIFFRACTIONr_angle_other_deg1.2741.5826463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33420.853129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.215521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0961522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.020.023016
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02566
LS refinement shellResolution: 1.58→1.621 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 221 -
Rwork0.186 4409 -
all-4630 -
obs--98.93 %

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