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- PDB-3ls2: Crystal structure of an S-formylglutathione hydrolase from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 3ls2
TitleCrystal structure of an S-formylglutathione hydrolase from Pseudoalteromonas haloplanktis TAC125
ComponentsS-formylglutathione Hydrolase
KeywordsHYDROLASE / S-formylglutathione hydrolase / psychrophilic organism / Pseudoalteromonas haloplanktis
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-formylglutathione hydrolase
Similarity search - Component
Biological speciesPseudoalteromonas haloplanktis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAlterio, V. / De Simone, G.
CitationJournal: Biopolymers / Year: 2010
Title: Crystal structure of an S-formylglutathione hydrolase from Pseudoalteromonas haloplanktis TAC125.
Authors: Alterio, V. / Aurilia, V. / Romanelli, A. / Parracino, A. / Saviano, M. / D'Auria, S. / De Simone, G.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: S-formylglutathione Hydrolase
B: S-formylglutathione Hydrolase
C: S-formylglutathione Hydrolase
D: S-formylglutathione Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8058
Polymers123,6634
Non-polymers1424
Water18,9881054
1
A: S-formylglutathione Hydrolase
B: S-formylglutathione Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9024
Polymers61,8312
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: S-formylglutathione Hydrolase
D: S-formylglutathione Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9024
Polymers61,8312
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.49, 129.75, 152.67
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
S-formylglutathione Hydrolase


Mass: 30915.732 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria)
Strain: TAC125 / Gene: PSHAa1385 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q3IL66, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1054 / 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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (w/v) PEG MME 5000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 10, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 49990 / Num. obs: 49990 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 5.9 / Num. unique all: 4666 / % possible all: 93.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PV1

1pv1


Resolution: 2.2→20 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2434 -RANDOM
Rwork0.161 ---
obs-48748 95.9 %-
Displacement parametersBiso mean: 15.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8656 0 4 1054 9714
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4

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