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- PDB-5g59: Structure of the Pyrococcus Furiosus Esterase Pf2001 with space g... -

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Basic information

Entry
Database: PDB / ID: 5g59
TitleStructure of the Pyrococcus Furiosus Esterase Pf2001 with space group P3121
ComponentsESTERASE
KeywordsSTRUCTURAL PROTEIN / 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 / SAD / Resolution: 1.613 Å
AuthorsVarejao, N. / Reverter, D.
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
DepositionMay 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
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 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1653
Polymers31,7641
Non-polymers4012
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.334, 105.334, 47.843
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2114-

HOH

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Components

#1: Protein ESTERASE /


Mass: 31763.531 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8TZJ1
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETION OF THE 20 FIRST RESIDUES

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 44.2 % / Description: NONE
Crystal growDetails: 30% MPD, 10% PEG 4000, 0.1 M IMIDAZOLE-HCL, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9998
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.61→52.66 Å / Num. obs: 39571 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 17.7 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 15.7
Reflection shellResolution: 1.61→1.62 Å / Redundancy: 17.6 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.613→52.667 Å / SU ML: 0.14 / σ(F): 1.37 / Phase error: 17.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 1913 4.8 %
Rwork0.167 --
obs0.1683 39550 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.613→52.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 2 153 2392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062309
X-RAY DIFFRACTIONf_angle_d1.0583129
X-RAY DIFFRACTIONf_dihedral_angle_d12.359850
X-RAY DIFFRACTIONf_chiral_restr0.046326
X-RAY DIFFRACTIONf_plane_restr0.005395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6131-1.65350.21651430.19432669X-RAY DIFFRACTION100
1.6535-1.69820.21921230.182658X-RAY DIFFRACTION100
1.6982-1.74820.19851200.17672665X-RAY DIFFRACTION100
1.7482-1.80460.19911460.18212654X-RAY DIFFRACTION100
1.8046-1.86910.23491440.16922668X-RAY DIFFRACTION100
1.8691-1.94390.19581410.16512665X-RAY DIFFRACTION100
1.9439-2.03240.19771400.16712677X-RAY DIFFRACTION100
2.0324-2.13950.20011340.16392677X-RAY DIFFRACTION100
2.1395-2.27360.18281420.16462678X-RAY DIFFRACTION100
2.2736-2.44910.21821320.17262687X-RAY DIFFRACTION100
2.4491-2.69560.20341510.17322677X-RAY DIFFRACTION100
2.6956-3.08560.21161280.17582704X-RAY DIFFRACTION100
3.0856-3.88740.17881710.16152695X-RAY DIFFRACTION100
3.8874-52.69510.1532980.15052863X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 86.1932 Å / Origin y: 73.1231 Å / Origin z: 48.8675 Å
111213212223313233
T0.0835 Å2-0.0067 Å20.005 Å2-0.0596 Å20.0085 Å2--0.0767 Å2
L1.1483 °20.4685 °20.2221 °2-1.0126 °20.3719 °2--0.8845 °2
S-0.0413 Å °0.0485 Å °0.0024 Å °-0.0382 Å °0.0483 Å °-0.0526 Å °0.0236 Å °-0.0516 Å °-0.0023 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESSEQ -10:9999)

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