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- PDB-4q05: Crystal structure of an esterase E25 -

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Basic information

Entry
Database: PDB / ID: 4q05
TitleCrystal structure of an esterase E25
Componentsesterase E25
KeywordsHYDROLASE / esterase
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lipolytic enzyme
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLi, P.Y. / Li, C.Y. / Zhang, Y.Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural basis for dimerization and catalysis of a novel esterase from the GTSAG motif subfamily of the bacterial hormone-sensitive lipase family
Authors: Li, P.Y. / Ji, P. / Li, C.Y. / Zhang, Y. / Wang, G.L. / Zhang, X.Y. / Xie, B.B. / Qin, Q.L. / Chen, X.L. / Zhou, B.C. / Zhang, Y.Z.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Other
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Downloads & links

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Assembly

Deposited unit
A: esterase E25
B: esterase E25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9836
Polymers77,8922
Non-polymers924
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-71 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.796, 138.796, 49.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein esterase E25


Mass: 38945.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: B8Y553*PLUS
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KJ624992 FOR THIS SEQUENCE.

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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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 0.2M sodium acetate trihydrate, 0.1M sodium cacodylate trihydrate, 17% PEG8,000, pH 6.5, EVAPORATION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 64925 / Num. obs: 64925 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.05→2.12 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet derivatives

Resolution: 2.05→19.807 Å / SU ML: 0.21 / σ(F): 1.96 / Phase error: 21.39 / Stereochemistry target values: Overall
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 3283 5.07 %RANDOM
Rwork0.1678 ---
obs0.169 64693 97.1 %-
all-64693 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.818 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0511 Å2-0 Å20 Å2
2---0.0511 Å20 Å2
3---0.1023 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 0 4 577 5569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075141
X-RAY DIFFRACTIONf_angle_d1.0377025
X-RAY DIFFRACTIONf_dihedral_angle_d11.1421869
X-RAY DIFFRACTIONf_chiral_restr0.067815
X-RAY DIFFRACTIONf_plane_restr0.005920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.05-2.07870.24241400.2242267698
2.0787-2.11110.26231390.2099267698
2.1111-2.14570.27861390.2141265396
2.1457-2.18270.25771510.2104269699
2.1827-2.22230.24761460.2071265396
2.2223-2.2650.2971460.1996270398
2.265-2.31120.2471310.2031264996
2.3112-2.36130.27381390.1903268796
2.3613-2.41620.20051290.1945261897
2.4162-2.47650.21531270.2015270896
2.4765-2.54330.22291380.1969263197
2.5433-2.6180.24281500.1981265196
2.618-2.70230.22561490.1966262796
2.7023-2.79860.19611580.1941264197
2.7986-2.91030.20161350.1932262995
2.9103-3.04230.21811430.187262796
3.0423-3.20210.18231360.1696267596
3.2021-3.40180.19911540.1637262296
3.4018-3.66290.16771380.1521265897
3.6629-4.02870.16951480.1432269298
4.0287-4.60530.13241340.12812771100
4.6053-5.77820.15021500.13532730100
5.7782-19.80750.15461630.14682737100

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