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- PDB-4peo: Crystal structure of a hypothetical protein from Staphylococcus a... -

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Basic information

Entry
Database: PDB / ID: 4peo
TitleCrystal structure of a hypothetical protein from Staphylococcus aureus.
ComponentsHypothetical protein
KeywordsUNKNOWN FUNCTION / conserved hypothetical protein
Function / homology
Function and homology information


cysteine-type peptidase activity / ribosome biogenesis / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis
Similarity search - Function
Cysteine protease Prp / Cysteine protease Prp / Cysteine protease Prp superfamily / Cysteine protease Prp / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Ribosomal processing cysteine protease Prp
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsMcGrath, T.E. / Kisselman, G. / Romanov, V. / Wu-Brown, J. / Soloveychik, M. / Chan, T.S.Y. / Gordon, R.D. / Thambipillai, D. / Dharamsi, A. / Mansoury, K. ...McGrath, T.E. / Kisselman, G. / Romanov, V. / Wu-Brown, J. / Soloveychik, M. / Chan, T.S.Y. / Gordon, R.D. / Thambipillai, D. / Dharamsi, A. / Mansoury, K. / Battaile, K.P. / Edwards, A.M. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: To Be Published
Title: Crystal structure of a hypothetical protein from Staphylococcus aureus.
Authors: McGrath, T.E. / Kisselman, G. / Romanov, V. / Wu-Brown, J. / Soloveychik, M. / Chan, T.S.Y. / Gordon, R.D. / Thambipillai, D. / Dharamsi, A. / Mansoury, K. / Battaile, K.P. / Edwards, A.M. / ...Authors: McGrath, T.E. / Kisselman, G. / Romanov, V. / Wu-Brown, J. / Soloveychik, M. / Chan, T.S.Y. / Gordon, R.D. / Thambipillai, D. / Dharamsi, A. / Mansoury, K. / Battaile, K.P. / Edwards, A.M. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
SupersessionMay 13, 2015ID: 2P92
Revision 1.1May 13, 2015Group: Other
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid
Revision 1.3Feb 28, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)23,4042
Polymers23,4042
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-17 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.205, 67.205, 127.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Hypothetical protein


Mass: 11701.829 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: N6IJW4, UniProt: Q2FXS9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 31% PEG400, 0.2M Magnesium chloride, 0.1M HEPES, pH7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 22209 / Num. obs: 22209 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.033 / Χ2: 1.039 / Net I/σ(I): 17.8
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.35 / Num. unique all: 2230 / Χ2: 1.077 / % possible all: 99.5

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P92

2p92
PDB Unreleased entry


Resolution: 1.73→18.87 Å / Cor.coef. Fo:Fc: 0.9539 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 1135 5.11 %RANDOM
Rwork0.1858 ---
obs0.1871 22195 99.21 %-
Displacement parametersBiso mean: 35.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.0635 Å20 Å20 Å2
2--1.0635 Å20 Å2
3----2.127 Å2
Refine analyzeLuzzati coordinate error obs: 0.245 Å
Refinement stepCycle: 1 / Resolution: 1.73→18.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 0 108 1507
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011413HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.991926HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d488SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes207HARMONIC5
X-RAY DIFFRACTIONt_it1413HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion15.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion211SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1693SEMIHARMONIC4
LS refinement shellResolution: 1.73→1.81 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2486 166 5.62 %
Rwork0.2319 2789 -
all0.2329 2955 -
obs--99.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.03-0.38720.54571.7189-0.80844.54630.0235-0.01360.06450.01350.1120.1143-0.2753-0.2638-0.1355-0.01020.04970.0367-0.07260.0377-0.0608-9.788116.763132.5963
22.3066-0.7548-0.55561.15050.75765.60060.0379-0.17150.1146-0.12910.03520.0039-0.0673-0.1258-0.0731-0.05010.02740.0494-0.06490.0125-0.0749-11.204917.682453.3686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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