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- PDB-2wkw: Alcaligenes esterase complexed with product analogue -

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Basic information

Entry
Database: PDB / ID: 2wkw
TitleAlcaligenes esterase complexed with product analogue
ComponentsCARBOXYLESTERASE
KeywordsHYDROLASE / HYDROLASE(CARBOXYLIC ESTERASE) / ESTERASE / ATOMIC RESOLUTION / ALPHA/BETA HYDROLASE
Function / homology: / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-W22 / Carboxylesterase
Function and homology information
Biological speciesALCALIGENES SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsBourne, P.C. / Isupov, M.N. / Littlechild, J.A.
Citation
Journal: Structure / Year: 2000
Title: The Atomic-Resolution Structure of a Novel Bacterial Esterase.
Authors: Bourne, P.C. / Isupov, M.N. / Littlechild, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Novel Bacterial Esterase
Authors: Bourne, P.C. / Isupov, M.N. / Littlechild, J.A.
History
DepositionJun 18, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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: CARBOXYLESTERASE
B: CARBOXYLESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,15918
Polymers71,3742
Non-polymers1,78616
Water12,611700
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-120.35 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.597, 115.811, 131.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.97218, -0.01039, -0.234), (0.00315, -0.9995, 0.03131), (-0.23421, 0.0297, 0.97173)
Vector: 8.01847, 73.07857, -0.18449)

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Components

#1: Protein CARBOXYLESTERASE / ESTERASE


Mass: 35686.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALCALIGENES SP. (bacteria) / Production host: AGROBACTERIUM SP. (bacteria) / References: UniProt: Q7SIA5
#2: Chemical ChemComp-W22 / [(2S)-4-methyl-3-oxo-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-2-yl]acetic acid


Mass: 234.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 3.02 Å3/Da / Density % sol: 54.42 % / Description: NONE
Crystal growpH: 7 / Details: 30% (NH4)2SO4, 10 MM TRIS HCL, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 2.03→20 Å / Num. obs: 57445 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 2.03→2.06 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLW

1qlw


Resolution: 2.03→19.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.06 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE CRYSTALS WERE SOAKED WITH THE PRODUCT ANALOGUE IODINATED AT THE PHENOL RING. HOWEVER NO TRACE OF IODINATION WAS OBSERVED IN THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 2910 5.1 %RANDOM
Rwork0.15498 ---
obs0.157 54468 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.412 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å20 Å2
2---2.37 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.03→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 111 700 5641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225188
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9787094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91223.679212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61315812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6681531
X-RAY DIFFRACTIONr_chiral_restr0.0840.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223967
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.02143199
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9665185
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4781989
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.424101890
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 211 -
Rwork0.184 3942 -
obs--100 %

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