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- PDB-5cml: Crystal structure of the Esterase domain from Rhodothermus marinu... -

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Basic information

Entry
Database: PDB / ID: 5cml
TitleCrystal structure of the Esterase domain from Rhodothermus marinus Rmar_1206 protein
ComponentsOsmC family protein
KeywordsHYDROLASE / Serine Esterase OsmC Thermophile
Function / homology
Function and homology information


OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / K homology domain-like, alpha/beta / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / OsmC family protein
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsMarles-Wright, J. / Wardrope, C. / Jensen, M.-B.V. / Horsfall, L.E. / Togneri, P.D. / Rosser, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Plos One / Year: 2016
Title: Characterisation of a New Family of Carboxyl Esterases with an OsmC Domain.
Authors: Jensen, M.V. / Horsfall, L.E. / Wardrope, C. / Togneri, P.D. / Marles-Wright, J. / Rosser, S.J.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,3364
Polymers58,0362
Non-polymers3002
Water5,044280
1
A: OsmC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1682
Polymers29,0181
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OsmC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1682
Polymers29,0181
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.325, 74.069, 60.953
Angle α, β, γ (deg.)90.00, 113.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein OsmC family protein / esterase Rmar_1206


Mass: 29018.025 Da / Num. of mol.: 2 / Fragment: UNP residues 1-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus (bacteria) / Gene: Rmar_1206 / Plasmid: pDest17 / Production host: Escherichia coli (E. coli) / Strain (production host): AI / References: UniProt: D0MHY8
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein at 15 mg/ml was crystallized by sitting drop vapour diffusion with 100 nl drops of protein supplemented with 100 nl of mother liquor comprising 0.2 M ammonium citrate dibasic, pH 5. ...Details: Protein at 15 mg/ml was crystallized by sitting drop vapour diffusion with 100 nl drops of protein supplemented with 100 nl of mother liquor comprising 0.2 M ammonium citrate dibasic, pH 5.0, 20 % w/v PEG 3350 (Hampton PEG/Ion HT96 screen D12), drops were equilibrated against 70 ul of mother liquor for one month before crystals appeared.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 25, 2013
RadiationMonochromator: Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→44.62 Å / Num. all: 255878 / Num. obs: 69888 / % possible obs: 99.09 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.91
Reflection shellResolution: 1.56→1.612 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 1.88 / % possible all: 98.48

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FUK, 3TRD, 3PF9

2fuk

3trd

3pf9


Resolution: 1.56→44.62 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 3544 5.07 %Random Selection
Rwork0.1442 ---
obs0.1458 69880 99.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3584 0 20 280 3884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013710
X-RAY DIFFRACTIONf_angle_d1.1795032
X-RAY DIFFRACTIONf_dihedral_angle_d13.2451355
X-RAY DIFFRACTIONf_chiral_restr0.047579
X-RAY DIFFRACTIONf_plane_restr0.006659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.556-1.57730.32511320.29452572X-RAY DIFFRACTION97
1.5773-1.59990.30171500.25612660X-RAY DIFFRACTION100
1.5999-1.62370.29681390.22312653X-RAY DIFFRACTION100
1.6237-1.64910.25521150.19742674X-RAY DIFFRACTION100
1.6491-1.67620.24741620.17362646X-RAY DIFFRACTION100
1.6762-1.70510.20471410.16092652X-RAY DIFFRACTION100
1.7051-1.73610.21781500.14722657X-RAY DIFFRACTION100
1.7361-1.76950.16691220.14062706X-RAY DIFFRACTION100
1.7695-1.80560.1911370.13442654X-RAY DIFFRACTION100
1.8056-1.84480.19571570.13392686X-RAY DIFFRACTION100
1.8448-1.88770.17241350.12662646X-RAY DIFFRACTION100
1.8877-1.9350.17571330.12432655X-RAY DIFFRACTION100
1.935-1.98730.18861300.12622687X-RAY DIFFRACTION100
1.9873-2.04580.16961700.12892616X-RAY DIFFRACTION100
2.0458-2.11180.16991510.12512685X-RAY DIFFRACTION100
2.1118-2.18730.17431470.12312659X-RAY DIFFRACTION100
2.1873-2.27480.15421410.1232674X-RAY DIFFRACTION100
2.2748-2.37840.17931390.12192666X-RAY DIFFRACTION100
2.3784-2.50370.16321420.12352661X-RAY DIFFRACTION99
2.5037-2.66060.18111330.13842681X-RAY DIFFRACTION99
2.6606-2.8660.17061550.14612602X-RAY DIFFRACTION98
2.866-3.15430.20351330.15132612X-RAY DIFFRACTION97
3.1543-3.61060.15151490.14212607X-RAY DIFFRACTION97
3.6106-4.54820.15141450.14022632X-RAY DIFFRACTION97
4.5482-44.64270.181360.16082693X-RAY DIFFRACTION97

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