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- PDB-4fp7: 2.2A resolution structure of Proteasome Assembly Chaperone Hsm3 -

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Basic information

Entry
Database: PDB / ID: 4fp7
Title2.2A resolution structure of Proteasome Assembly Chaperone Hsm3
ComponentsDNA mismatch repair protein HSM3
KeywordsCHAPERONE / Hsm3 / Proteasome
Function / homology
Function and homology information


proteasome regulatory particle assembly / mismatch repair / protein folding chaperone / nucleus / cytoplasm / cytosol
Similarity search - Function
Leucine-rich Repeat Variant - #50 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #580 / DNA mismatch repair protein HSM3, C-terminal domain / DNA mismatch repair protein HSM3, N-terminal domain / DNA mismatch repair protein HSM3, C terminal domain / DNA mismatch repair protein HSM3, N terminal domain / Leucine-rich Repeat Variant / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
DNA mismatch repair protein HSM3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.2 Å
AuthorsLovell, S. / Battaile, K.P. / Singh, R. / Zolkiewski, M. / Roelofs, J.
CitationJournal: To be Published
Title: 2.2A resolution structure of Proteasome Assembly Chaperone Hsm3
Authors: Singh, R. / Lovell, S. / Zolkiewski, M. / Battaile, K.P. / Roelofs, J.
History
DepositionJun 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: DNA mismatch repair protein HSM3
B: DNA mismatch repair protein HSM3


Theoretical massNumber of molelcules
Total (without water)113,3712
Polymers113,3712
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-14 kcal/mol
Surface area38110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.148, 94.466, 129.931
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains two biological units

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Components

#1: Protein DNA mismatch repair protein HSM3 / Enhanced spontaneous mutability protein 3


Mass: 56685.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HSM3, YBR272C, YBR1740 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P38348
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 4000, 100 mM Hepes, 150 mM ammonium sulfate, pH 7.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→129.93 Å / Num. all: 53064 / Num. obs: 53064 / % possible obs: 98.56 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.75 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.0771
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.2-2.326.930.662.9752673760397.78
2.32-2.466.820.464.4749028719298.14
2.46-2.636.680.326.4645609682498.43
2.63-2.846.860.23943464633398.35
2.84-3.117.120.1413.4842026590599.12
3.11-3.486.860.0919.5936698535198.96
3.48-4.026.380.0627.6230363475798.95
4.02-4.926.620.0436.4526881405999.18
4.92-6.966.260.0432.3619991319499.23
6.96-129.936.080.0341.7611224184698.27

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å71.22 Å
Translation2.5 Å71.22 Å

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
PHASER2.4.0phasing
PHENIXdev_906refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→44.391 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.19 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2663 5.06 %RANDOM
Rwork0.188 ---
obs0.1906 53012 98.06 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.07 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 94.07 Å2 / Biso mean: 37.0421 Å2 / Biso min: 9.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.4688 Å2-0 Å20 Å2
2---2.4645 Å20 Å2
3---0.9957 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7025 0 0 261 7286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017148
X-RAY DIFFRACTIONf_angle_d1.1259688
X-RAY DIFFRACTIONf_chiral_restr0.0611144
X-RAY DIFFRACTIONf_plane_restr0.0051223
X-RAY DIFFRACTIONf_dihedral_angle_d14.1652652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.31981580.28813174333297
2.225-2.25120.37391480.28133206335497
2.2512-2.27860.33981970.27173091328897
2.2786-2.30750.36991460.26583216336297
2.3075-2.33780.35371910.25863111330298
2.3378-2.36990.31111600.25063204336497
2.3699-2.40370.2831770.24053160333798
2.4037-2.43960.27781600.21373156331697
2.4396-2.47770.27491980.20133173337199
2.4777-2.51830.28231750.1923212338798
2.5183-2.56170.23091710.18583187335898
2.5617-2.60830.25141650.18123164332999
2.6083-2.65850.23491640.17923222338698
2.6585-2.71270.24551760.181232203396100
2.7127-2.77170.25131960.18983182337898
2.7717-2.83620.24091660.18373187335398
2.8362-2.90710.26861470.19133215336299
2.9071-2.98570.28011650.20123245341099
2.9857-3.07350.29311960.21143147334398
3.0735-3.17270.29941650.2083266343199
3.1727-3.28610.25331480.2083203335199
3.2861-3.41760.26831800.19643204338498
3.4176-3.57310.22161710.18043200337198
3.5731-3.76130.21521880.16693167335598
3.7613-3.99690.20081590.15433195335498
3.9969-4.30520.17491740.14343178335298
4.3052-4.7380.18211620.13983241340399
4.738-5.42260.18921620.15643180334298
5.4226-6.82790.20441610.20173212337398
6.8279-44.39990.20971750.18783170334597

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