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- PDB-7kkf: Crystal Structure of S. cerevisiae Ess1 -

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Basic information

Entry
Database: PDB / ID: 7kkf
TitleCrystal Structure of S. cerevisiae Ess1
ComponentsPeptidyl-prolyl cis-trans isomerase ESS1
KeywordsISOMERASE / Ess1 / prolyl isomerase / transcription
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nucleus
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNamitz, K.E.W. / Alicea-Velazquez, N.L. / Cosgrove, M.S. / Hanes, S.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123985 United States
National Science Foundation (NSF, United States)1750462 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA140522 United States
CitationJournal: Commun Biol / Year: 2021
Title: Structure analysis suggests Ess1 isomerizes the carboxy-terminal domain of RNA polymerase II via a bivalent anchoring mechanism.
Authors: Namitz, K.E.W. / Zheng, T. / Canning, A.J. / Alicea-Velazquez, N.L. / Castaneda, C.A. / Cosgrove, M.S. / Hanes, S.D.
History
DepositionOct 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase ESS1
B: Peptidyl-prolyl cis-trans isomerase ESS1


Theoretical massNumber of molelcules
Total (without water)38,7432
Polymers38,7432
Non-polymers00
Water50428
1
A: Peptidyl-prolyl cis-trans isomerase ESS1


Theoretical massNumber of molelcules
Total (without water)19,3721
Polymers19,3721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase ESS1


Theoretical massNumber of molelcules
Total (without water)19,3721
Polymers19,3721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.098, 57.366, 69.334
Angle α, β, γ (deg.)90.000, 96.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase ESS1 / SX2_G0029750.mRNA.1.CDS.1 / Y55_G0030090.mRNA.1.CDS.1


Mass: 19371.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS3553, PACBIOSEQ_LOCUS3670, PACBIOSEQ_LOCUS3692
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6L0ZJ56, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.92 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris, pH 7.7 and 21% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.392→50 Å / Num. obs: 16821 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 49.83 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.04 / Rrim(I) all: 0.107 / Χ2: 2.601 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4970.71216940.8940.2860.7681.616100
2.49-2.597.10.59816400.9340.2390.6451.661100
2.59-2.770.45616710.9610.1830.4921.7699.9
2.7-2.8570.3116810.9770.1240.3341.83199.8
2.85-3.0270.20716640.9890.0830.2232.02299.9
3.02-3.267.20.13116850.9930.0520.1412.35499.9
3.26-3.587.20.09516710.9940.0380.1032.91499.9
3.58-4.170.07716980.9960.0310.0833.487100
4.1-5.176.90.0716960.9960.0280.0754.02100
5.17-506.60.0717210.9960.030.0764.40498.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YW5

1yw5


Resolution: 2.4→29.21 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3065 823 4.92 %
Rwork0.2693 15918 -
obs0.2712 16741 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.14 Å2 / Biso mean: 56.7417 Å2 / Biso min: 33.74 Å2
Refinement stepCycle: final / Resolution: 2.4→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 0 28 2372
Biso mean---52.11 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082374
X-RAY DIFFRACTIONf_angle_d1.0063187
X-RAY DIFFRACTIONf_dihedral_angle_d5.2111449
X-RAY DIFFRACTIONf_chiral_restr0.053339
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.550.40011310.34642496262794
2.55-2.750.42451370.35662661279899
2.75-3.020.41421330.36692645277899
3.02-3.460.32851340.284426852819100
3.46-4.360.27481400.241826842824100
4.36-29.210.26571480.233627472895100

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