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- PDB-4fhz: Crystal structure of a carboxyl esterase at 2.0 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 4fhz
TitleCrystal structure of a carboxyl esterase at 2.0 angstrom resolution
ComponentsPhospholipase/Carboxylesterase
KeywordsHYDROLASE / esterase / alpha/beta hydrolase superfamily / central beta-stranded sheet / flanked alpha helices / Structural Genomics
Function / homology
Function and homology information


Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Phospholipase/Carboxylesterase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsWu, L. / Ma, J. / Zhou, J. / Yu, H.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2013
Title: Enhanced enantioselectivity of a carboxyl esterase from Rhodobacter sphaeroides by directed evolution.
Authors: Ma, J. / Wu, L. / Guo, F. / Gu, J. / Tang, X. / Jiang, L. / Liu, J. / Zhou, J. / Yu, H.
History
DepositionJun 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Feb 28, 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_ref_seq_dif / 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_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _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: Phospholipase/Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1739
Polymers29,9061
Non-polymers2678
Water1,62190
1
A: Phospholipase/Carboxylesterase
hetero molecules

A: Phospholipase/Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,34618
Polymers59,8122
Non-polymers53416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area1510 Å2
ΔGint-12 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.042, 72.042, 113.583
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Phospholipase/Carboxylesterase


Mass: 29905.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cell / Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: CGMCC1.1737 / Gene: RSP_2728 / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3J2V1, carboxylesterase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.65 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 3M sodium chloride, citric acid,1% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 23303 / Num. obs: 23109 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 18.128
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible all
2-2.0791100
2.07-2.159.11100
2.15-2.259.11100
2.25-2.379.1199.8
2.37-2.5291100
2.52-2.718.81100
2.71-2.998.4199.8
2.99-3.427.5199.9
3.42-4.317199.4
4.31-506.9194.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.01→34.336 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 17.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 1191 5.15 %
Rwork0.1589 --
obs0.1616 23106 99.1 %
all-2750 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.309 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8644 Å20 Å20 Å2
2---0.8644 Å2-0 Å2
3---1.7288 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.36 Å
Luzzati sigma a0.31 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.01→34.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 14 90 1715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061763
X-RAY DIFFRACTIONf_angle_d0.922420
X-RAY DIFFRACTIONf_dihedral_angle_d12.445668
X-RAY DIFFRACTIONf_chiral_restr0.067266
X-RAY DIFFRACTIONf_plane_restr0.005328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.09010.25781270.17792353X-RAY DIFFRACTION98
2.0901-2.18520.20611270.1412437X-RAY DIFFRACTION100
2.1852-2.30030.20741390.12032383X-RAY DIFFRACTION100
2.3003-2.44440.19941560.14352427X-RAY DIFFRACTION100
2.4444-2.63310.23521290.15522427X-RAY DIFFRACTION100
2.6331-2.8980.25571380.17772438X-RAY DIFFRACTION100
2.898-3.3170.2611410.17862447X-RAY DIFFRACTION100
3.317-4.17790.19771180.15032505X-RAY DIFFRACTION100
4.1779-34.34070.18741160.16072498X-RAY DIFFRACTION95

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