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- PDB-4he5: Crystal structure of the selenomethionine variant of the C-termin... -

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Basic information

Entry
Database: PDB / ID: 4he5
TitleCrystal structure of the selenomethionine variant of the C-terminal domain of Geobacillus thermoleovorans putative U32 peptidase
ComponentsPeptidase family U32
KeywordsUNKNOWN FUNCTION / Ultra-tight crystal packing
Function / homology
Function and homology information


: / peptidase activity / proteolysis
Similarity search - Function
Peptidase family U32, C-terminal / Peptidase family U32 C-terminal domain / Peptidase family U32 signature. / Peptidase U32 / Peptidase family U32 / Translation factors / Ribulose-phosphate binding barrel / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesGeobacillus thermoleovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsTrillo-Muyo, S. / Jasilionis, A. / Domagalski, M.J. / Chruszcz, M. / Minor, W. / Kuisiene, N. / Arolas, J.L. / Sola, M. / Gomis-Ruth, F.X.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Ultratight crystal packing of a 10 kDa protein.
Authors: Trillo-Muyo, S. / Jasilionis, A. / Domagalski, M.J. / Chruszcz, M. / Minor, W. / Kuisiene, N. / Arolas, J.L. / Sola, M. / Gomis-Ruth, F.X.
History
DepositionOct 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase family U32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5992
Polymers10,5031
Non-polymers961
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.550, 45.550, 60.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

21A-655-

HOH

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Components

#1: Protein Peptidase family U32


Mass: 10502.541 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP Residues 334-422)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermoleovorans (bacteria) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8N3E1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.75 Å3/Da / Density % sol: 29.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M tri-sodium citrate, 2 M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2012
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.15→39.5 Å / Num. all: 26349 / Num. obs: 26349 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036
Reflection shellResolution: 1.15→1.21 Å

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Processing

Software
NameClassification
ProDCdata collection
SHELXmodel building
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→33 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.17 792 random
Rwork0.141 --
all0.141 25557 -
obs0.141 25557 -
Refinement stepCycle: LAST / Resolution: 1.15→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms680 0 5 74 759
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.44
LS refinement shellResolution: 1.15→1.21 Å
RfactorNum. reflection% reflection
Rfree0.17 792 -
Rwork0.141 --
obs-25557 99.7 %

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