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- PDB-7dxs: Crystal structure of the ap1h peptide homodimer. -

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Basic information

Entry
Database: PDB / ID: 7dxs
TitleCrystal structure of the ap1h peptide homodimer.
Componentsap1h protein
KeywordsCHAPERONE / Double psi beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsYagi, S. / Tagami, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H01328 Japan
Citation
Journal: J.Am.Chem.Soc. / Year: 2021
Title: Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.
Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S.
#1: Journal: Biorxiv / Year: 2021
Title: Seven amino acid types suffice to reconstruct the core fold of RNA polymerase.
Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ap1h protein
B: ap1h protein
C: ap1h protein
D: ap1h protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,18113
Polymers21,3164
Non-polymers8659
Water2,036113
1
A: ap1h protein
B: ap1h protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0426
Polymers10,6582
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-71 kcal/mol
Surface area4960 Å2
MethodPISA
2
C: ap1h protein
D: ap1h protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1387
Polymers10,6582
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-81 kcal/mol
Surface area5260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.716, 40.431, 56.300
Angle α, β, γ (deg.)90.000, 91.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
ap1h protein


Mass: 5329.073 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG4000, 170mM Ammonium sulfate, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 11344 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 17.76
Reflection shellResolution: 2.1→2.23 Å / Num. unique obs: 1776 / CC1/2: 0.938

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DXR

7dxr


Resolution: 2.102→33.663 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 1120 9.87 %
Rwork0.1886 10222 -
obs0.1921 11342 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.57 Å2 / Biso mean: 30.9593 Å2 / Biso min: 14.43 Å2
Refinement stepCycle: final / Resolution: 2.102→33.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 45 113 1561
Biso mean--53.04 39.13 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.102-2.19730.27491290.2218122498
2.1973-2.31310.26421360.20881275100
2.3131-2.4580.2511450.20631269100
2.458-2.64770.24561410.20791273100
2.6477-2.9140.24321330.20261295100
2.914-3.33540.23781410.1921277100
3.3354-4.20090.20711440.15991283100
4.2009-33.6630.18871510.1821326100

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