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- PDB-4ccy: Crystal structure of carboxylesterase CesB (YbfK) from Bacillus s... -

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Basic information

Entry
Database: PDB / ID: 4ccy
TitleCrystal structure of carboxylesterase CesB (YbfK) from Bacillus subtilis
Components(CARBOXYLESTERASE YBFK) x 2
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity / cytoplasm
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
Carboxylesterase YbfK
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 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 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 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 YBFK
B: CARBOXYLESTERASE YBFK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3136
Polymers66,2212
Non-polymers924
Water8,179454
1
A: CARBOXYLESTERASE YBFK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1653
Polymers33,1191
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CARBOXYLESTERASE YBFK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1493
Polymers33,1031
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.110, 44.010, 108.660
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-2250-

HOH

21B-2193-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 12 - 294 / Label seq-ID: 11 - 293

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.3145, 0.001922, -0.9493), (0.003592, -1, -0.000835), (-0.9493, -0.003147, -0.3145)
Vector: 67.49, -0.4117, 93.2)

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Components

#1: Protein CARBOXYLESTERASE YBFK / CARBOXYLESTERASE CESB


Mass: 33118.539 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Plasmid: PBAD/MYC-HISA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: O31452, carboxylesterase
#2: Protein CARBOXYLESTERASE YBFK / CARBOXYLESTERASE CESB


Mass: 33102.539 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Plasmid: PBAD/MYC-HISA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: O31452, carboxylesterase
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: SITTING DROPS WITH 20% PEG3350, 0.2M SODIUM FLUORIDE, 100 MM BIS-TRIS PROPANE BUFFER, pH 6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 5, 2011 / Details: HELIOSMX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→46 Å / Num. obs: 47148 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.1
Reflection shellResolution: 2.04→2.14 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.9 / % possible all: 76.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CCW

4ccw


Resolution: 2.04→108.6 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.309 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25013 2395 5.1 %RANDOM
Rwork0.20362 ---
obs0.20599 44660 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.127 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.41 Å2
2---0.22 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.04→108.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4501 0 4 454 4959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194623
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9466281
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7015568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70423.832214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27915739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7941524
X-RAY DIFFRACTIONr_chiral_restr0.0830.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213558
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1128medium positional0.060.5
2B1104loose positional0.45
1A1128medium thermal0.822
2B1104loose thermal0.9610
LS refinement shellResolution: 2.038→2.091 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 132 -
Rwork0.277 2482 -
obs--72.33 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
118.0463-0.80827.32284.56451.15637.43750.1234-0.0592-0.19820.0762-0.23860.2620.5325-0.5180.11520.0687-0.05940.02670.07830.00470.092548.3692-16.323653.9956
22.0674-0.53370.10341.1494-0.08170.86760.0134-0.1813-0.04610.0939-0.0428-0.00770.054-0.01750.02940.0176-0.00850.01140.03990.01590.03657.8041-4.372160.7859
31.44760.0385-0.45050.71710.03281.3166-0.0151-0.01770.0916-0.0022-0.04540.0391-0.1007-0.01670.06050.01010.0041-0.00460.01960.0020.059960.01657.383353.5169
46.0672-1.2270.14922.6164-2.42622.4283-0.02480.2676-0.324-0.18860.04820.08020.1912-0.1052-0.02350.07020.0196-0.0390.0886-0.02020.067555.6022-9.690136.45
53.2882-2.15180.0342.76020.54191.79260.1970.1558-0.1803-0.0886-0.21830.07250.0821-0.05710.02130.025-0.0034-0.02120.028-0.0050.074955.084-12.886546.1062
61.1959-0.33780.39081.0787-0.24421.08980.01640.0590.0328-0.074-0.0287-0.0935-0.01230.08590.01230.0072-0.0030.01230.04170.01640.059569.76874.315547.08
76.3057-2.9612.08046.0642-3.379618.3086-0.0079-0.63930.38280.35970.02870.3136-0.2111-0.3016-0.02080.11670.00420.05130.0901-0.06510.078331.05416.030130.4807
80.960.0919-0.36290.8593-0.4832.30620.01040.03720.0788-0.02780.00590.118-0.0593-0.1864-0.01630.05480.03210.00850.03920.00140.02827.70934.044519.41
90.8494-0.00760.03731.05340.00831.163-0.01080.0431-0.09520.0734-0.00350.00660.0514-0.0010.01430.08830.01520.00540.04790.00370.012637.2806-621.0776
103.9395-4.56052.50365.5779-1.45198.68660.07060.09810.0726-0.0639-0.0328-0.10650.04120.5186-0.03780.1239-0.0608-0.02170.06540.02090.091448.081113.810922.04
112.87131.6105-0.51914.43-2.34964.18110.0205-0.30710.13020.2453-0.1489-0.1757-0.1765-0.20760.12830.141-0.0220.010.0604-0.02160.028937.755811.449631.5104
120.8970.01090.19471.0443-0.13221.47520.01210.0384-0.0368-0.0362-0.0688-0.07250.01280.09710.05670.0690.01650.00950.03760.00410.0144.5716-4.600512.3558
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 26
2X-RAY DIFFRACTION2A27 - 102
3X-RAY DIFFRACTION3A103 - 166
4X-RAY DIFFRACTION4A167 - 185
5X-RAY DIFFRACTION5A186 - 213
6X-RAY DIFFRACTION6A214 - 294
7X-RAY DIFFRACTION7B11 - 26
8X-RAY DIFFRACTION8B27 - 102
9X-RAY DIFFRACTION9B103 - 175
10X-RAY DIFFRACTION10B176 - 195
11X-RAY DIFFRACTION11B196 - 213
12X-RAY DIFFRACTION12B214 - 294

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