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- PDB-4rot: Crystal structure of esterase A from Streptococcus pyogenes -

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Basic information

Entry
Database: PDB / ID: 4rot
TitleCrystal structure of esterase A from Streptococcus pyogenes
ComponentsEsterase A
KeywordsHYDROLASE / hydrolase esterase acyltransferase / acylglycerase / hydrolysis
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / OXALATE ION / :
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsBennett, M.D. / Holland, R. / Coulibaly, F. / Loo, T.S. / Norris, G.E. / Anderson, B.F.
CitationJournal: To be Published
Title: Crystal structure of esterase A from Streptococcus pyogenes
Authors: Bennett, M.D. / Holland, R. / Coulibaly, F. / Loo, T.S. / Norris, G.E. / Anderson, B.F.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Assembly

Deposited unit
A: Esterase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0133
Polymers30,8601
Non-polymers1532
Water5,855325
1
A: Esterase A
hetero molecules

A: Esterase A
hetero molecules

A: Esterase A
hetero molecules

A: Esterase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,05212
Polymers123,4394
Non-polymers6148
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation15_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area14870 Å2
ΔGint-49 kcal/mol
Surface area36570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.980, 103.980, 133.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-301-

ZN

21A-302-

OXL

31A-302-

OXL

41A-408-

HOH

51A-520-

HOH

61A-540-

HOH

71A-679-

HOH

81A-719-

HOH

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Components

#1: Protein Esterase A


Mass: 30859.648 Da / Num. of mol.: 1 / Mutation: L156N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: Est A, HMPREF1245_1265 / Plasmid: pProEXHTb SPyTBEsterase / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V6W522, carboxylesterase, arylesterase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 20% PEG4000, 10% 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.93937
SYNCHROTRONESRF ID2920.93957
SYNCHROTRONESRF ID2930.89844
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDSep 24, 2005Toroidal Mirror
ADSC QUANTUM 2102CCDSep 24, 2005Toroidal Mirror
ADSC QUANTUM 2103CCDSep 24, 2005Toroidal Mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1high resolution Si(311) cutSINGLE WAVELENGTHMx-ray1
2high resolution Si(311) cutSINGLE WAVELENGTHMx-ray1
3high resolution Si(311) cutSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.939371
20.939571
30.898441
ReflectionResolution: 1.75→15 Å / Num. all: 37068 / Num. obs: 37068 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.4
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.496 / Num. unique all: 3658 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.8.0073refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→14.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.896 / SU ML: 0.061 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19319 1724 5.1 %RANDOM
Rwork0.15759 ---
all0.15941 34036 --
obs0.15941 32310 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2--0.03 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→14.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 7 325 2505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192281
X-RAY DIFFRACTIONr_bond_other_d0.0020.022073
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.9373098
X-RAY DIFFRACTIONr_angle_other_deg1.00834773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.795279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.77924.661118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80715376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.746158
X-RAY DIFFRACTIONr_chiral_restr0.1370.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
X-RAY DIFFRACTIONr_mcbond_it1.7271.2211086
X-RAY DIFFRACTIONr_mcbond_other1.7261.221085
X-RAY DIFFRACTIONr_mcangle_it2.6251.821360
X-RAY DIFFRACTIONr_mcangle_other2.6241.821361
X-RAY DIFFRACTIONr_scbond_it2.4551.4311195
X-RAY DIFFRACTIONr_scbond_other2.461.4141189
X-RAY DIFFRACTIONr_scangle_other3.8092.0241727
X-RAY DIFFRACTIONr_long_range_B_refined6.31711.3312950
X-RAY DIFFRACTIONr_long_range_B_other5.95710.6052803
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 112 -
Rwork0.189 2331 -
obs-2331 99.39 %

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