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- PDB-5hh7: crystal structure of Arabidopsis ORC1b BAH-PHD cassette in comple... -

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Basic information

Entry
Database: PDB / ID: 5hh7
Titlecrystal structure of Arabidopsis ORC1b BAH-PHD cassette in complex with unmodified H3 peptide
Components
  • Histone H3 1-15 peptide
  • Origin of replication complex subunit 1B
KeywordsTRANSCRIPTION / PHD finger / BAH domain / multivalent readout
Function / homology
Function and homology information


double fertilization forming a zygote and endosperm / origin recognition complex / chromocenter / double-stranded methylated DNA binding / nuclear origin of replication recognition complex / mitotic DNA replication checkpoint signaling / plastid / DNA replication origin binding / DNA replication initiation / structural constituent of chromatin ...double fertilization forming a zygote and endosperm / origin recognition complex / chromocenter / double-stranded methylated DNA binding / nuclear origin of replication recognition complex / mitotic DNA replication checkpoint signaling / plastid / DNA replication origin binding / DNA replication initiation / structural constituent of chromatin / nucleosome / histone binding / DNA replication / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / extracellular region / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Origin recognition complex, subunit 1 / AAA lid domain / AAA lid domain / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. ...Origin recognition complex, subunit 1 / AAA lid domain / AAA lid domain / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / ATPase family associated with various cellular activities (AAA) / Histone H3 signature 1. / ATPase, AAA-type, core / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3.1 / Origin of replication complex subunit 1B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsLi, S. / Du, J.
CitationJournal: Structure / Year: 2016
Title: Structural Basis for the Unique Multivalent Readout of Unmodified H3 Tail by Arabidopsis ORC1b BAH-PHD Cassette
Authors: Li, S. / Yang, Z. / Du, X. / Liu, R. / Wilkinson, A.W. / Gozani, O. / Jacobsen, S.E. / Patel, D.J. / Du, J.
History
DepositionJan 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Origin of replication complex subunit 1B
P: Histone H3 1-15 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0984
Polymers28,9672
Non-polymers1312
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint2 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.408, 64.408, 79.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Origin of replication complex subunit 1B / / AtORC1b / Origin recognition complex 1b protein / Protein UNFERTILIZED EMBRYO SAC 13


Mass: 27401.057 Da / Num. of mol.: 1 / Fragment: BAH-PHD cassette, UNP residues 118-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ORC1B, UNE13, At4g12620, T1P17.210 / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9SU24
#2: Protein/peptide Histone H3 1-15 peptide


Mass: 1565.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P59226*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.86 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Na-formate and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2827 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Number: 184019 / Rmerge(I) obs: 0.092 / Χ2: 3.31 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 25599 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.095010.0718.0676.6
3.254.0910.0756.046.7
2.843.2510.0894.8027
2.582.8410.1073.4267.3
2.392.5810.1272.817.4
2.252.3910.1572.3287.4
2.142.2510.1962.0297.4
2.052.1410.2511.6847.4
1.972.0510.3451.4377.4
1.91.9710.4911.2987.4
ReflectionResolution: 1.9→50 Å / Num. obs: 25599 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.092 / Χ2: 3.306 / Net I/av σ(I): 46.324 / Net I/σ(I): 14 / Num. measured all: 184019
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.977.40.49125241.29899.6
1.97-2.057.40.34525381.43799.5
2.05-2.147.40.25125511.68499.8
2.14-2.257.40.19625532.02999.8
2.25-2.397.40.15725432.32899.8
2.39-2.587.40.12725702.8199.9
2.58-2.847.30.10725573.426100
2.84-3.2570.08925634.802100
3.25-4.096.70.07525816.04100
4.09-506.60.07126198.06799.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→45.543 Å / FOM work R set: 0.8747 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 20.1 / Stereochemistry target values: ML
Details: ANOMALOUS DATA WAS USED FOR REFINEMENT. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2047 2565 5.13 %
Rwork0.1943 47421 -
obs0.1948 25576 99.27 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.682 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 106.39 Å2 / Biso mean: 40.82 Å2 / Biso min: 16.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.9133 Å2-0 Å20 Å2
2---0.9133 Å20 Å2
3---1.8266 Å2
Refinement stepCycle: final / Resolution: 1.901→45.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 2 189 1866
Biso mean--61.15 40.36 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031724
X-RAY DIFFRACTIONf_angle_d0.8582318
X-RAY DIFFRACTIONf_chiral_restr0.062238
X-RAY DIFFRACTIONf_plane_restr0.003299
X-RAY DIFFRACTIONf_dihedral_angle_d14.315661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9006-1.93720.33741380.27552635277399
1.9372-1.97670.25481250.24122610273599
1.9767-2.01970.21421320.22122691282399
2.0197-2.06670.2321400.21372567270799
2.0667-2.11840.27981700.20692645281599
2.1184-2.17560.23511660.19782587275399
2.1756-2.23970.23831040.20462665276999
2.2397-2.31190.27041320.199226932825100
2.3119-2.39460.20211530.199326172770100
2.3946-2.49040.18991590.19432663282299
2.4904-2.60380.21061770.209525972774100
2.6038-2.7410.24011460.213226262772100
2.741-2.91270.20271500.20432643279399
2.9127-3.13760.20281580.19282590274899
3.1376-3.45320.24451270.19522677280499
3.4532-3.95270.17721450.1812620276599
3.9527-4.9790.13561370.14972645278299
4.979-45.55640.21781060.20992650275699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.74061.18482.34521.6579-0.41373.8411-0.12330.1290.4339-0.11310.1358-1.10520.2540.7289-0.06350.20920.0726-0.03060.3267-0.08880.5645-7.388812.541911.1828
25.1175-1.0706-2.89821.77242.70086.34630.227-0.9049-0.6622-0.07930.28260.43250.22220.1127-0.42850.7893-0.10860.06110.45470.09120.5963-22.75924.26387.4197
32.50890.13870.71293.12293.21783.86450.11790.2758-0.7184-0.4242-0.39550.5070.6585-0.01270.19741.0846-0.1853-0.18170.38760.03890.9184-31.0722.1507-14.4878
42.436-0.17670.03061.2887-0.30311.91510.12610.4018-0.4971-0.75380.13170.30321.1733-0.4665-0.1430.5429-0.1172-0.09870.2989-0.03490.3432-31.221912.3417-11.9544
51.4236-0.5830.38141.9122-0.27871.2438-0.0265-0.19780.02290.03950.1021-0.26990.05170.0947-0.05270.1705-0.006-0.01050.2313-0.02010.2165-20.600520.02778.2885
62.9178-0.36140.74956.794-0.53484.10360.10580.06940.0551-0.2654-0.1416-0.4150.98340.5606-0.16410.47160.04980.01040.2315-0.03620.2639-20.341910.0808-9.5437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 128:150)A128 - 150
2X-RAY DIFFRACTION2chain 'A' and (resseq 151:166)A151 - 166
3X-RAY DIFFRACTION3chain 'A' and (resseq 167:176)A167 - 176
4X-RAY DIFFRACTION4chain 'A' and (resseq 177:247)A177 - 247
5X-RAY DIFFRACTION5chain 'A' and (resseq 248:344)A248 - 344
6X-RAY DIFFRACTION6chain 'P' and (resseq 1:9)P1 - 9

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