PDB-5g5c: Structure of the Pyrococcus furiosus Esterase Pf2001 with space g...

ID or keywords:

Entry

Database: PDB / ID: 5g5c

Title

Structure of the Pyrococcus furiosus Esterase Pf2001 with space group C2221

Components

ESTERASE

Keywords

STRUCTURAL PROTEIN / ESTERASE / THEMOPHILIC

Function / homology

: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / Serine aminopeptidase S33 domain-containing protein

Function and homology information

Biological species

PYROCOCCUS FURIOSUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.18 Å

Authors

Varejao, N. / Reverter, D.

Citation

Journal: 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

Deposition	May 23, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 21, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Data collection / Structure summary / Category: diffrn_detector / struct / Item: _diffrn_detector.type / _struct.title
Revision 1.2	Jan 17, 2018	Group: 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 1.3	Feb 14, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4	Jan 10, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5g5c.cif.gz	120.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5g5c.ent.gz	93.9 KB	Display	PDB format
PDBx/mmJSON format	5g5c.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5g5c_validation.pdf.gz	423.3 KB	Display	wwPDB validaton report
Full document	5g5c_full_validation.pdf.gz	425.8 KB	Display
Data in XML	5g5c_validation.xml.gz	12.5 KB	Display
Data in CIF	5g5c_validation.cif.gz	17.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g5/5g5c ftp://data.pdbj.org/pub/pdb/validation_reports/g5/5g5c	HTTPS FTP

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Related structure data

Related structure data	5g59SC 5g5mC 5lcnC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5lcn-2 2bnd-d 5lcn-1 7l6p-d 4o7r-1 4o7t-1 5u10-d 4o86-1 5fya-d 5zdb-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ESTERASE

31.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ESTERASE

defined by author&software
63.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.596, 72.915, 135.929
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-2003- HOH

#1: Protein	ESTERASE Mass: 31763.531 Da / Num. of mol.: 1 / Fragment: YES, 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.9 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.18→135.92 Å / Num. obs: 79722 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / R_merge(I) obs: 0.04 / Net I/σ(I): 19.9
Reflection shell	Resolution: 1.18→1.18 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.4_1496)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G59

5g59

Resolution: 1.18→40.438 Å / SU ML: 0.1 / σ(F): 1.35 / Phase error: 17.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.192	3863	4.9 %
R_work	0.1779	-	-
obs	0.1786	79503	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.18→40.438 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2139	0	0	157	2296

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2227
X-RAY DIFFRACTION	f_angle_d	1.109	3019
X-RAY DIFFRACTION	f_dihedral_angle_d	12.875	832
X-RAY DIFFRACTION	f_chiral_restr	0.048	318
X-RAY DIFFRACTION	f_plane_restr	0.006	378

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.18-1.1944	0.2867	142	0.2745	2628	X-RAY DIFFRACTION	100
1.1944-1.2095	0.2136	145	0.2469	2674	X-RAY DIFFRACTION	100
1.2095-1.2254	0.2353	132	0.2428	2652	X-RAY DIFFRACTION	100
1.2254-1.2422	0.2552	142	0.2356	2689	X-RAY DIFFRACTION	100
1.2422-1.26	0.2333	139	0.2164	2680	X-RAY DIFFRACTION	100
1.26-1.2788	0.2389	152	0.2138	2678	X-RAY DIFFRACTION	100
1.2788-1.2988	0.2491	127	0.2013	2658	X-RAY DIFFRACTION	100
1.2988-1.32	0.2055	149	0.198	2698	X-RAY DIFFRACTION	100
1.32-1.3428	0.2368	138	0.1959	2641	X-RAY DIFFRACTION	100
1.3428-1.3672	0.2035	152	0.1913	2692	X-RAY DIFFRACTION	100
1.3672-1.3935	0.1851	141	0.1868	2654	X-RAY DIFFRACTION	100
1.3935-1.422	0.1811	135	0.187	2695	X-RAY DIFFRACTION	100
1.422-1.4529	0.1871	139	0.1806	2698	X-RAY DIFFRACTION	100
1.4529-1.4867	0.1912	134	0.1762	2681	X-RAY DIFFRACTION	100
1.4867-1.5239	0.1925	129	0.1753	2695	X-RAY DIFFRACTION	100
1.5239-1.5651	0.185	127	0.1719	2720	X-RAY DIFFRACTION	100
1.5651-1.6111	0.2119	131	0.169	2670	X-RAY DIFFRACTION	100
1.6111-1.6631	0.1709	134	0.1711	2709	X-RAY DIFFRACTION	100
1.6631-1.7226	0.1797	142	0.1727	2692	X-RAY DIFFRACTION	100
1.7226-1.7916	0.1853	129	0.1738	2696	X-RAY DIFFRACTION	100
1.7916-1.8731	0.1958	147	0.172	2710	X-RAY DIFFRACTION	100
1.8731-1.9718	0.1758	144	0.1666	2710	X-RAY DIFFRACTION	100
1.9718-2.0954	0.1988	124	0.1681	2750	X-RAY DIFFRACTION	100
2.0954-2.2571	0.1702	136	0.1745	2708	X-RAY DIFFRACTION	100
2.2571-2.4843	0.1776	115	0.1766	2765	X-RAY DIFFRACTION	100
2.4843-2.8437	0.2196	143	0.181	2743	X-RAY DIFFRACTION	100
2.8437-3.5824	0.1807	149	0.1773	2767	X-RAY DIFFRACTION	100
3.5824-40.4616	0.1814	146	0.1619	2887	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Origin x: -14.0206 Å / Origin y: -16.7855 Å / Origin z: 18.1594 Å

	11	12	13	21	22	23	31	32	33
T	0.0848 Å²	-0.0278 Å²	0.014 Å²	-	0.0944 Å²	-0.0145 Å²	-	-	0.0834 Å²
L	0.8013 °²	0.1482 °²	0.0334 °²	-	0.7792 °²	-0.1042 °²	-	-	0.6288 °²
S	0.0452 Å °	-0.1166 Å °	0.0117 Å °	0.079 Å °	-0.044 Å °	-0.0028 Å °	-0.0107 Å °	-0.0374 Å °	-0.0019 Å °

Refinement TLS group

Selection details: (CHAIN A AND RESSEQ 21:288)

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