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- PDB-4s1p: Shel_16390 protein, a putative SGNH hydrolase from Slackia heliot... -

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Basic information

Entry
Database: PDB / ID: 4s1p
TitleShel_16390 protein, a putative SGNH hydrolase from Slackia heliotrinireducens
ComponentsUncharacterized protein
KeywordsHYDROLASE / structural genomics / APC103766 / SGNH hydrolase / unknown ligand / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologySGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Unknown ligand / SGNH hydrolase-type esterase domain-containing protein
Function and homology information
Biological speciesSlackia heliotrinireducens DSM 20476 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsOsipiuk, J. / Cuff, M.E. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Shel_16390 protein, a putative SGNH hydrolase from Slackia heliotrinireducens
Authors: Osipiuk, J. / Cuff, M.E. / Wu, R. / Endres, M. / Joachimiak, A.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)20,4162
Polymers20,4161
Non-polymers01
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.591, 67.023, 71.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 20415.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Slackia heliotrinireducens DSM 20476 (bacteria)
Strain: DSM 20476 / Gene: Shel_16390 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7N6X3
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 1.5 M lithium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→35.3 Å / Num. all: 35098 / Num. obs: 35098 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.143 / Χ2: 3.302 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.45-1.483.30.6541.9515441.17788.9
1.48-1.53.60.61816471.31594.3
1.5-1.534.20.52517171.48198.1
1.53-1.5650.48317491.66199.8
1.56-1.65.40.43917341.81599.9
1.6-1.635.70.417742.08100
1.63-1.676.20.37517252.385100
1.67-1.726.80.34417492.43699.7
1.72-1.776.80.31817522.69299.5
1.77-1.836.90.28817493.12499.9
1.83-1.896.90.24817453.11299.8
1.89-1.976.90.2217703.13599.8
1.97-2.066.90.20717573.3799.9
2.06-2.1770.19117873.44699.9
2.17-2.37.10.17817713.78100
2.3-2.487.10.16717753.848100
2.48-2.737.20.15517953.884100
2.73-3.127.10.13318134.242100
3.12-3.9470.10718284.43399.9
3.94-506.50.09619177.58798.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXCDphasing
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→35.3 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.909 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1559 1769 5 %RANDOM
Rwork0.1176 ---
obs0.1195 33266 98.52 %-
all-33266 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.32 Å2 / Biso mean: 19.369 Å2 / Biso min: 10.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-0 Å2
2---1.26 Å2-0 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.45→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 9 200 1544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191486
X-RAY DIFFRACTIONr_bond_other_d0.0010.021439
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9962039
X-RAY DIFFRACTIONr_angle_other_deg0.8233322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3835215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21423.27961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96715210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7511513
X-RAY DIFFRACTIONr_chiral_restr0.090.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
X-RAY DIFFRACTIONr_mcbond_it1.4921.586775
X-RAY DIFFRACTIONr_mcbond_other1.4941.581774
X-RAY DIFFRACTIONr_mcangle_it1.8712.391978
X-RAY DIFFRACTIONr_rigid_bond_restr3.2332925
X-RAY DIFFRACTIONr_sphericity_free27.833559
X-RAY DIFFRACTIONr_sphericity_bonded8.2153026
LS refinement shellResolution: 1.447→1.485 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 106 -
Rwork0.228 2098 -
all-2204 -
obs-2204 85.59 %

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