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- PDB-5lcn: STRUCTURE OF THE PYROCOCCUS FURIOSUS ESTERASE PF2001 WITH SPACE G... -

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Basic information

Entry
Database: PDB / ID: 5lcn
TitleSTRUCTURE OF THE PYROCOCCUS FURIOSUS ESTERASE PF2001 WITH SPACE GROUP P212121
ComponentsUncharacterized protein
KeywordsHYDROLASE / ESTERASE / THEMOPHILIC
Function / homologySerine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / Serine aminopeptidase S33 domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVarejao, N. / Reverter, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-66417-P Spain
CitationJournal: Structure / Year: 2018
Title: Structural Mechanism for the Temperature-Dependent Activation of the Hyperthermophilic Pf2001 Esterase.
Authors: Varejao, N. / De-Andrade, R.A. / Almeida, R.V. / Anobom, C.D. / Foguel, D. / Reverter, D.
History
DepositionJun 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.5Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.6Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)127,5316
Polymers127,0544
Non-polymers4772
Water1,47782
1
A: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7653
Polymers63,5272
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-28 kcal/mol
Surface area21150 Å2
MethodPISA
2
B: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7653
Polymers63,5272
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-29 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.495, 99.440, 146.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Uncharacterized protein


Mass: 31763.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF2001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZJ1
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 8000, 10% Ethylene glycol, 0.1 M HEPES sodium salt, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.59→48.25 Å / Num. obs: 38776 / % possible obs: 87.7 % / Redundancy: 4.2 % / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5g59

5g59


Resolution: 2.6→48.248 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1948 5.04 %
Rwork0.1956 --
obs0.1987 38617 87.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8645 0 32 82 8759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038934
X-RAY DIFFRACTIONf_angle_d0.71912083
X-RAY DIFFRACTIONf_dihedral_angle_d12.7253319
X-RAY DIFFRACTIONf_chiral_restr0.0281270
X-RAY DIFFRACTIONf_plane_restr0.0041514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6650.29511290.24862509X-RAY DIFFRACTION85
2.665-2.73710.31871330.25022659X-RAY DIFFRACTION90
2.7371-2.81760.3321470.24922660X-RAY DIFFRACTION90
2.8176-2.90850.38321450.24732617X-RAY DIFFRACTION89
2.9085-3.01250.26181340.22512651X-RAY DIFFRACTION89
3.0125-3.13310.33091460.23772601X-RAY DIFFRACTION89
3.1331-3.27560.29331500.22672625X-RAY DIFFRACTION89
3.2756-3.44830.28171300.21342658X-RAY DIFFRACTION89
3.4483-3.66430.27511360.19912641X-RAY DIFFRACTION89
3.6643-3.94710.24161460.1792611X-RAY DIFFRACTION88
3.9471-4.34410.22311480.16282596X-RAY DIFFRACTION87
4.3441-4.97210.19151390.15112608X-RAY DIFFRACTION87
4.9721-6.26220.22181210.17462623X-RAY DIFFRACTION86
6.2622-48.25580.22041440.18112610X-RAY DIFFRACTION82

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