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- PDB-3r0v: The crystal structure of an alpha/beta hydrolase from Sphaerobact... -

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Basic information

Entry
Database: PDB / ID: 3r0v
TitleThe crystal structure of an alpha/beta hydrolase from Sphaerobacter thermophilus DSM 20745.
ComponentsAlpha/beta hydrolase fold protein
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / MCSG / alpha/beta hydrolase / Midwest Center for Structural Genomics
Function / homology
Function and homology information


: / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / D-MALATE / Alpha/beta hydrolase fold protein
Similarity search - Component
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.383 Å
AuthorsTan, K. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of an alpha/beta hydrolase from Sphaerobacter thermophilus DSM 20745.
Authors: Tan, K. / Wu, R. / Clancy, S. / Joachimiak, A.
History
DepositionMar 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: 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 / struct_site
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 / _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: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3286
Polymers27,9101
Non-polymers4185
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.220, 72.162, 45.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha/beta hydrolase fold protein


Mass: 27910.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / S 6022 / Gene: Sphaerobacter thermophilus, Sthe_2971 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: D1C982

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Non-polymers , 5 types, 304 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.9 Å3/Da / Density % sol: 35.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M CaCl2, 0.1M HEPES:NaOH, 30% (w/v) PEG 4000, pH 7.5, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.38→38 Å / Num. all: 44078 / Num. obs: 44078 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 34
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1672 / % possible all: 95.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.383→37.076 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 17.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 2141 5.05 %random
Rwork0.1634 ---
obs0.1645 42410 95.9 %-
all-42410 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.231 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4919 Å20 Å2-0 Å2
2--0.3151 Å20 Å2
3----3.807 Å2
Refinement stepCycle: LAST / Resolution: 1.383→37.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 24 299 2220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072043
X-RAY DIFFRACTIONf_angle_d1.1782815
X-RAY DIFFRACTIONf_dihedral_angle_d11.945762
X-RAY DIFFRACTIONf_chiral_restr0.073317
X-RAY DIFFRACTIONf_plane_restr0.009380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.383-1.43240.27821770.2573433X-RAY DIFFRACTION83
1.4324-1.48980.26951920.22263743X-RAY DIFFRACTION90
1.4898-1.55760.23692090.19043899X-RAY DIFFRACTION94
1.5576-1.63970.18792200.16373961X-RAY DIFFRACTION96
1.6397-1.74240.20242210.16144063X-RAY DIFFRACTION98
1.7424-1.8770.17442150.16224141X-RAY DIFFRACTION99
1.877-2.06580.17992400.15654138X-RAY DIFFRACTION100
2.0658-2.36470.16642260.15964209X-RAY DIFFRACTION100
2.3647-2.97910.19012130.16884252X-RAY DIFFRACTION100
2.9791-37.08920.17062280.14954430X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 47.8165 Å / Origin y: 10.1777 Å / Origin z: 5.0956 Å
111213212223313233
T0.1088 Å2-0.0034 Å20.0003 Å2-0.1148 Å20.0009 Å2--0.1128 Å2
L0.1188 °20.0398 °2-0.0017 °2-0.2175 °20.0767 °2--0.0361 °2
S0.0167 Å °-0.0054 Å °0.0086 Å °0.0023 Å °-0.0082 Å °0.0049 Å °-0.0002 Å °0.0024 Å °-0.0043 Å °
Refinement TLS groupSelection details: chain A

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