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- PDB-7l0a: Crystal structure of s-formylglutathione hydrolase (FrmB) from St... -

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Basic information

Entry
Database: PDB / ID: 7l0a
TitleCrystal structure of s-formylglutathione hydrolase (FrmB) from Staphylococcus aureus, apoenzyme
ComponentsEsterase family protein
KeywordsHYDROLASE / FrmB
Function / homology
Function and homology information


S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity / cytosol
Similarity search - Function
S-formylglutathione hydrolase / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
S-formylglutathione hydrolase / S-formylglutathione hydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMiller, J.J. / Jez, J.M. / Odom John, A.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI103280 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI123808 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI130584 United States
Citation
Journal: Elife / Year: 2021
Title: Structure-guided microbial targeting of antistaphylococcal prodrugs.
Authors: Miller, J.J. / Shah, I.T. / Hatten, J. / Barekatain, Y. / Mueller, E.A. / Moustafa, A.M. / Edwards, R.L. / Dowd, C.S. / Planet, P.J. / Muller, F.L. / Jez, J.M. / Odom John, A.R.
#1: Journal: Biorxiv / Year: 2020
Title: Structure-guided microbial targeting of antistaphylococcal prodrugs
Authors: Miller, J.J. / Shah, I.T. / Hatten, J. / Barekatain, Y. / Mueller, E.A. / Moustafa, A.M. / Edwards, R.L. / Dowd, C.S. / Planet, P.J. / Muller, F.L. / Jez, J.M.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase family protein
B: Esterase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9365
Polymers59,8632
Non-polymers733
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-44 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.303, 80.500, 66.651
Angle α, β, γ (deg.)90.000, 113.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-461-

HOH

31A-591-

HOH

41A-598-

HOH

51B-401-

HOH

61B-488-

HOH

71B-604-

HOH

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Components

#1: Protein Esterase family protein / Prolyl oligopeptidase family serine peptidase / Putative esterase / S-formylglutathione hydrolase / ...Prolyl oligopeptidase family serine peptidase / Putative esterase / S-formylglutathione hydrolase / Tributyrin esterase


Mass: 29931.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: DD547_02660, DQV53_15175, EP54_00010, EQ90_02595, G0V24_06825, G0Z18_09875, G6Y10_06490, GO746_05055, GO803_04470, GO805_09630, GO821_02780, GO894_07900, GO942_11740, HMPREF2819_04260, ...Gene: DD547_02660, DQV53_15175, EP54_00010, EQ90_02595, G0V24_06825, G0Z18_09875, G6Y10_06490, GO746_05055, GO803_04470, GO805_09630, GO821_02780, GO894_07900, GO942_11740, HMPREF2819_04260, HMPREF3211_01237, NCTC10654_02801, NCTC10702_04070, NCTC10988_03042, RK64_00235
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0D6GS23, UniProt: Q2FUY3*PLUS, S-formylglutathione hydrolase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 20 uL hanging drops containing a 1:1 mixture of protein (6 mg/mL) and crystallization buffer (0.1 M Tricine pH 7.7, 15% PEG6K, 2.5 M NaCl, 0.125% n-dodecyl-B-D-glucoside)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 78193 / % possible obs: 96.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.054 / Rrim(I) all: 0.093 / Χ2: 2.643 / Net I/σ(I): 11.7 / Num. measured all: 217757
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.415 / Num. unique obs: 3961 / CC1/2: 0.992 / Rpim(I) all: 0.034 / Rrim(I) all: 0.059 / Χ2: 3.02 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Coot0.8.9.2 ELmodel building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RGY

4rgy


Resolution: 1.6→36.81 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 1998 2.56 %
Rwork0.157 76139 -
obs0.158 78137 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.29 Å2 / Biso mean: 27.79 Å2 / Biso min: 10.11 Å2
Refinement stepCycle: final / Resolution: 1.6→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 3 476 4565
Biso mean--15.9 37.36 -
Num. residues----503
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.22971260.19014854498085
1.64-1.680.19591480.18085610575899
1.68-1.730.24341460.1765574572099
1.73-1.790.20481460.16925552569898
1.79-1.850.18321430.16565435557895
1.85-1.930.26881390.20555320545994
1.93-2.010.20321480.16395622577098
2.01-2.120.19981440.16835519566397
2.12-2.250.19091410.16735353549495
2.25-2.430.17071390.16025296543592
2.43-2.670.17161460.15285532567897
2.67-3.060.15551450.1495539568497
3.06-3.850.15561410.14025363550494
3.85-36.810.16131460.15095570571696

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