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- PDB-2uz0: The Crystal crystal structure of the estA protein, a virulence fa... -

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Basic information

Entry
Database: PDB / ID: 2uz0
TitleThe Crystal crystal structure of the estA protein, a virulence factor estA protein from Streptococcus pneumonia
ComponentsTRIBUTYRIN ESTERASE
KeywordsHYDROLASE / ESTERASE / ALPHA/BETA HYDROLASE / A VIRULENCE FACTOR FOR LUNG INFECTION
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding
Similarity search - Function
: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tributyrin esterase / Tributyrin esterase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKim, M.H. / Kang, B.S. / Kim, K.J. / Oh, T.K.
CitationJournal: Proteins / Year: 2008
Title: The Crystal Structure of the Esta Protein, a Virulence Factor from Streptococcus Pneumoniae.
Authors: Kim, M.H. / Kang, B.S. / Kim, S. / Kim, K.J. / Lee, C.H. / Oh, B.C. / Park, S.C. / Oh, T.K.
History
DepositionApr 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIBUTYRIN ESTERASE
B: TRIBUTYRIN ESTERASE
C: TRIBUTYRIN ESTERASE
D: TRIBUTYRIN ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,27916
Polymers122,3984
Non-polymers88112
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12930 Å2
ΔGint-12.5 kcal/mol
Surface area42640 Å2
MethodPQS
Unit cell
Length a, b, c (Å)71.695, 72.128, 101.827
Angle α, β, γ (deg.)90.00, 94.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TRIBUTYRIN ESTERASE / ESTERASE


Mass: 30599.404 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q97S09, UniProt: A0A0H2UNZ8*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 %
Description: STARTING MODEL FOR MR WAS A PARTIALLY REFINED MODEL OF THE SEMET CRYSTAL AT A 1.9A.
Crystal growDetails: 10% (V/V) PEG 6000,8% (V/V) ETHYLENE GLYCOL,4% (V/V) 2-METHYL-2,4-PENTANEDIOL,10 MM CYSTEINE,0.1 M TRIS-HCL PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 113097 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.949 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 5662 5 %RANDOM
Rwork0.183 ---
obs0.184 107413 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20.55 Å2
2---0.42 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8108 0 54 563 8725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.94311390
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11351006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78423.99391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.103151364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2071532
X-RAY DIFFRACTIONr_chiral_restr0.0910.21188
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026405
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3180.24269
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.25664
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2602
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.111.55118
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11127981
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.08333924
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8964.53401
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 378
Rwork0.232 7607
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7928-0.03240.03290.43050.0270.3158-0.00240.0039-0.04610.0004-0.0003-0.04070.02370.00130.0027-0.0580.00330.0117-0.05260.00580.024831.5520.14544.639
20.88770.0903-0.19230.2579-0.02650.3666-0.00140.0612-0.066-0.0013-0.00850.0459-0.01270.00020.01-0.0651-0.00270.0068-0.04480.00080.031-2.6975.73740.213
30.65780.167-0.04530.57970.04810.88750.00230.11820.017-0.1141-0.0051-0.0079-0.07540.05130.0028-0.02870.00250.02300.0202-0.051926.79120.51914.028
41.12550.01320.0740.52640.0341.01130.03490.2256-0.2615-0.1059-0.05190.0940.1423-0.06050.017-0.0493-0.004-0.01810.0017-0.11990.030210.62-10.39710.337
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 257
2X-RAY DIFFRACTION2B-4 - 257
3X-RAY DIFFRACTION3C-4 - 253
4X-RAY DIFFRACTION4D-4 - 257

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