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- PDB-4ccw: Crystal structure of naproxen esterase (carboxylesterase NP) from... -

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Basic information

Entry
Database: PDB / ID: 4ccw
TitleCrystal structure of naproxen esterase (carboxylesterase NP) from Bacillus subtilis
ComponentsCARBOXYL ESTERASE NP
KeywordsHYDROLASE
Function / homology
Function and homology information


methyl indole-3-acetate esterase activity / carboxylesterase
Similarity search - Function
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
(2-hydroxyethoxy)acetic acid / Carboxyl esterase NP
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRozeboom, H.J. / Godinho, L.F. / Nardini, M. / Quax, W.J. / Dijkstra, B.W.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Crystal Structures of Two Bacillus Carboxylesterases with Different Enantioselectivities.
Authors: Rozeboom, H.J. / Godinho, L.F. / Nardini, M. / Quax, W.J. / Dijkstra, B.W.
History
DepositionOct 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYL ESTERASE NP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9912
Polymers33,8711
Non-polymers1201
Water3,963220
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.987, 46.987, 212.461
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2075-

HOH

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Components

#1: Protein CARBOXYL ESTERASE NP / CARBOXYLESTERASE NP


Mass: 33871.289 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: THAI I-8 / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): I-85 / References: UniProt: Q59248, carboxylesterase
#2: Chemical ChemComp-VKC / (2-hydroxyethoxy)acetic acid


Mass: 120.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growMethod: liquid diffusion / pH: 8
Details: LIQUID-LIQUID DIFFUSION WITH 80% PEG6000, 0.1 M TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 28534 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.4
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ZOI, 1IUN, 1C4X
Resolution: 1.75→39.97 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.935 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26678 1413 5.1 %RANDOM
Rwork0.22695 ---
obs0.22895 26175 96.4 %-
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 35.473 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.32 Å20 Å2
2--0.65 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 8 220 2518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9453216
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98123.628113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19315375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2491513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211831
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 76 -
Rwork0.247 1582 -
obs--88.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.17475.2267-0.740711.5865-0.31297.0661-0.0084-0.34170.01190.10910.06160.14580.3-0.4384-0.05310.34350.05780.010.26010.05660.066932.33861.123731.1793
214.73392.24972.07864.57532.58163.508-1.547-0.73220.4690.97740.9670.29720.22580.09740.580.70680.28610.00770.4683-0.05760.099931.336616.968333.2839
31.65610.2984-0.11731.63460.67721.85630.0621-0.29270.07590.37740.00320.12950.146-0.0229-0.06530.2668-0.00640.06610.13970.00620.123828.534717.477725.3904
40.994-0.0405-0.22821.1910.72181.50330.0023-0.09250.09910.23110.02090.20330.013-0.2614-0.02320.19930.01770.07580.14980.01750.240722.291919.6315.0083
52.2883-1.45660.12742.958-1.22623.7751-0.0974-0.15660.01410.18160.1005-0.17970.38320.3332-0.00310.15530.0385-0.0330.1318-0.03460.240641.15863.16689.7569
69.05016.2393.07766.589-0.72015.0446-0.09870.3725-0.42310.20670.1099-0.46590.0220.5259-0.01130.38670.1369-0.04460.1927-0.04080.127142.70386.118523.1675
718.9776-8.486629.91673.879-13.521347.40571.3893-1.5776-1.2677-0.4790.8290.68831.9575-2.7458-2.21830.72610.18040.03510.56880.22670.315424.6134-1.004216.6762
81.2634-0.11780.37982.2228-0.05951.1442-0.07460.04040.03380.05390.09380.0505-0.1362-0.0719-0.01920.1471-0.01920.01920.09620.00990.217629.454920.61923.2451
91.9649-0.3690.76362.81250.53233.2545-0.0425-0.09220.31020.39080.0055-0.2858-0.42750.13250.03690.2162-0.0553-0.00880.0636-0.03940.252238.847826.628213.0224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 25
2X-RAY DIFFRACTION2A26 - 39
3X-RAY DIFFRACTION3A40 - 100
4X-RAY DIFFRACTION4A101 - 162
5X-RAY DIFFRACTION5A163 - 189
6X-RAY DIFFRACTION6A190 - 206
7X-RAY DIFFRACTION7A207 - 217
8X-RAY DIFFRACTION8A218 - 260
9X-RAY DIFFRACTION9A261 - 293

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