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- PDB-3e0x: The crystal structure of a Lipase-esterase related protein from C... -

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Basic information

Entry
Database: PDB / ID: 3e0x
TitleThe crystal structure of a Lipase-esterase related protein from Clostridium acetobutylicum ATCC 824
ComponentsLipase-esterase related protein
Keywordsstructural genomics / unknown function / APC60309 / Lipase-esterase related protein / Clostridium acetobutylicum ATCC 824 / PSI-2 / midwest center for structural genomics / MCSG / Protein Structure Initiative
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
: / alpha/beta hydrolase fold / 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
ORTHO-XYLENE / Lipase-esterase related protein
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsTan, K. / Sather, A. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a Lipase-esterase related protein from Clostridium acetobutylicum ATCC 824
Authors: Tan, K. / Sather, A. / Cobb, G. / Joachimiak, A.
History
DepositionAug 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 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_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_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: Lipase-esterase related protein
B: Lipase-esterase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4734
Polymers55,2612
Non-polymers2122
Water13,583754
1
A: Lipase-esterase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7362
Polymers27,6301
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipase-esterase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7362
Polymers27,6301
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.611, 75.153, 68.206
Angle α, β, γ (deg.)90.00, 97.89, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAuthors state that the biological assembly is experimentally unknown. From molecular packing, the molecule is expected to be a monomer.

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Components

#1: Protein Lipase-esterase related protein


Mass: 27630.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CA_C0816 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q97KV0
#2: Chemical ChemComp-OXE / ORTHO-XYLENE


Mass: 106.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M LiCl 20% PEG3350, 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2008 / Details: Mirror
RadiationMonochromator: Si crystal 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.45→38.1 Å / Num. all: 75965 / Num. obs: 75965 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 28.9
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.28 / Num. unique all: 2968 / % possible all: 75.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→38.1 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.292 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18455 3810 5 %RANDOM
Rwork0.14318 ---
all0.14525 72029 --
obs0.14525 72029 96.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.368 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.01 Å2
2---0.02 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.45→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4001 0 16 754 4771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224110
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9915586
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1395541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.86426.557183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93415805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg35.774154
X-RAY DIFFRACTIONr_chiral_restr0.0950.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023038
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22031
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22887
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2593
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.262
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2211.52563
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76124080
X-RAY DIFFRACTIONr_scbond_it2.72631707
X-RAY DIFFRACTIONr_scangle_it3.9634.51478
X-RAY DIFFRACTIONr_rigid_bond_restr1.54434270
X-RAY DIFFRACTIONr_sphericity_free5.2593759
X-RAY DIFFRACTIONr_sphericity_bonded3.83534017
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 229 -
Rwork0.163 4190 -
obs-4419 75.86 %

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