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- PDB-2q4f: Ensemble refinement of the crystal structure of putative histidin... -

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Basic information

Entry
Database: PDB / ID: 2q4f
TitleEnsemble refinement of the crystal structure of putative histidine-containing phosphotransfer protein from rice, Ak104879
ComponentsHistidine-containing phosphotransfer protein 1
KeywordsSIGNALING PROTEIN / Ensemble Refinement / Refinement Methodology Development / AK104879 / PHOSPHORELAY MEDIATOR / HP1 / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


positive regulation of cytokinin-activated signaling pathway / cytokinin-activated signaling pathway / protein histidine kinase binding / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / nucleus / cytoplasm / cytosol
Similarity search - Function
Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / HPT domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histidine-containing phosphotransfer protein 2
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine-containing phosphotransfer protein 1
B: Histidine-containing phosphotransfer protein 1


Theoretical massNumber of molelcules
Total (without water)33,5622
Polymers33,5622
Non-polymers00
Water5,747319
1
A: Histidine-containing phosphotransfer protein 1


Theoretical massNumber of molelcules
Total (without water)16,7811
Polymers16,7811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine-containing phosphotransfer protein 1


Theoretical massNumber of molelcules
Total (without water)16,7811
Polymers16,7811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.558, 100.558, 69.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Number of models8

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Components

#1: Protein Histidine-containing phosphotransfer protein 1 / OsHP1


Mass: 16780.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Strain: cv. Japonica
Gene: HP1, AK104879, Os09g0567400, LOC_Os09g39400, OJ1155_H10.30
Plasmid: PVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) P(LACI+RARE) / References: UniProt: Q6VAK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.6 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1YVI.

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Data collection

DetectorType: APS-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 1YVI

1yvi


Resolution: 2→37.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2337234.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1yvi and the first data set in the deposited structure factor file for 1yvi ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1yvi and the first data set in the deposited structure factor file for 1yvi along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 8 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1248 5.1 %RANDOM
Rwork0.145 ---
obs0.145 24416 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.656 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 0 319 2500
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.352
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2-2.130.2571954.90.15538140.0184031400999.5
2.13-2.290.2442115.20.13238270.0174050403899.7
2.29-2.520.2232135.30.13338390.0154062405299.7
2.52-2.880.2472085.10.15438550.0174076406399.7
2.88-3.630.2072225.50.14638470.0144126406998.6
3.63-37.770.2011994.80.14639860.0144337418596.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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