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- PDB-4bzw: Complete crystal structure of the carboxylesterase Cest-2923 (lp_... -

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Basic information

Entry
Database: PDB / ID: 4bzw
TitleComplete crystal structure of the carboxylesterase Cest-2923 (lp_2923) from Lactobacillus plantarum WCFS1
ComponentsLIPASE/ESTERASE
KeywordsHYDROLASE / LACTIC ACID BACTERIA
Function / homology
Function and homology information


aminopeptidase activity / identical protein binding / metal ion binding
Similarity search - Function
: / BD-FAE / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / ACETATE ION / Lipase/esterase
Similarity search - Component
Biological speciesLACTOBACILLUS PLANTARUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.148 Å
AuthorsBenavente, R. / Esteban-Torres, M. / Acebron, I. / delasRivas, B. / Munoz, R. / Alvarez, Y. / Mancheno, J.M.
CitationJournal: FEBS J. / Year: 2013
Title: Structure, Biochemical Characterization and Analysis of the Pleomorphism of Carboxylesterase Cest-2923 from Lactobacillus Plantarum Wcfs1
Authors: Benavente, R. / Esteban-Torres, M. / Acebron, I. / De Las Rivas, B. / Munoz, R. / Alvarez, Y. / Mancheno, J.M.
History
DepositionJul 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Dec 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: LIPASE/ESTERASE
B: LIPASE/ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,71415
Polymers62,5512
Non-polymers1,16413
Water9,062503
1
A: LIPASE/ESTERASE
B: LIPASE/ESTERASE
hetero molecules

A: LIPASE/ESTERASE
B: LIPASE/ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,42930
Polymers125,1014
Non-polymers2,32826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area14170 Å2
ΔGint-278.8 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.655, 141.655, 165.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

21A-2012-

HOH

31A-2023-

HOH

41A-2092-

HOH

51A-2142-

HOH

61B-2008-

HOH

71B-2019-

HOH

81B-2083-

HOH

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Components

#1: Protein LIPASE/ESTERASE / CEST-2923


Mass: 31275.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS PLANTARUM (bacteria) / Strain: WCFS1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: F9US10, carboxylesterase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 3.8 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growpH: 4.6
Details: 1.7 M AMMONIUM SULPHATE, 0.15 M SODIUM ACETATE, PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.94
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.15→46.3 Å / Num. obs: 53876 / % possible obs: 99.9 % / Redundancy: 19.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.2
Reflection shellResolution: 2.15→2.26 Å / Redundancy: 18 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 6.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D3N
Resolution: 2.148→46.367 Å / SU ML: 0.17 / σ(F): 1.33 / Phase error: 18.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 2730 5.1 %
Rwork0.1556 --
obs0.1576 53770 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 2.148→46.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 65 503 4844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074508
X-RAY DIFFRACTIONf_angle_d16179
X-RAY DIFFRACTIONf_dihedral_angle_d14.5781570
X-RAY DIFFRACTIONf_chiral_restr0.073680
X-RAY DIFFRACTIONf_plane_restr0.004798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.148-2.1850.24991350.1862431X-RAY DIFFRACTION98
2.185-2.22480.24051460.17212502X-RAY DIFFRACTION100
2.2248-2.26760.26341080.22982505X-RAY DIFFRACTION98
2.2676-2.31380.21511240.1672541X-RAY DIFFRACTION100
2.3138-2.36420.22361400.16262492X-RAY DIFFRACTION100
2.3642-2.41910.20161350.15662516X-RAY DIFFRACTION100
2.4191-2.47960.20991370.1512533X-RAY DIFFRACTION100
2.4796-2.54670.17161450.14912510X-RAY DIFFRACTION100
2.5467-2.62160.18081530.15072526X-RAY DIFFRACTION100
2.6216-2.70620.20711360.15452505X-RAY DIFFRACTION100
2.7062-2.80290.21471430.16032542X-RAY DIFFRACTION100
2.8029-2.91510.22941230.16512546X-RAY DIFFRACTION100
2.9151-3.04780.21421330.17412561X-RAY DIFFRACTION100
3.0478-3.20840.21071410.1632559X-RAY DIFFRACTION100
3.2084-3.40940.21441480.15562552X-RAY DIFFRACTION100
3.4094-3.67250.19371250.13492585X-RAY DIFFRACTION100
3.6725-4.04190.14661360.12882601X-RAY DIFFRACTION100
4.0419-4.62640.14111380.12322611X-RAY DIFFRACTION100
4.6264-5.82690.1961440.14112640X-RAY DIFFRACTION100
5.8269-46.37830.18351400.19292782X-RAY DIFFRACTION98
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)
16.96284.9361-5.85218.4017-6.13265.6818-0.32060.3376-0.3014-0.5327-0.1364-0.0580.3052-0.55390.28040.11280.0447-0.00670.22330.00710.207-63.280541.6975-32.1331
27.4732-0.5449-6.3661.22720.36135.3064-0.01550.3101-0.1318-0.095-0.1403-0.01070.0461-0.44210.03860.1051-0.0298-0.01440.1119-0.00470.1561-59.436542.2306-30.3904
36.0719-5.84076.17476.431-6.48136.66220.94731.7825-0.8087-1.6921-1.1546-1.15121.74470.89910.13430.55380.04730.06650.4525-0.14520.5664-45.734334.2158-49.7778
43.0959-0.3144-1.8151.00260.4462.7325-0.0256-0.1109-0.021-0.0309-0.04720.0018-0.01520.01360.08480.1153-0.0288-0.01130.17390.02710.1705-53.571650.6067-31.0213
53.71971.4269-0.20932.927-3.38175.09410.1822-0.25620.23390.35670.01270.5808-0.0509-0.06130.02030.1553-0.0454-0.00080.2635-0.03830.2315-63.473451.3692-13.8303
62.3276-0.7988-0.62746.43965.7237.43870.1454-0.2618-0.31130.0332-0.2054-0.15020.0932-0.23840.09440.1084-0.0141-0.00170.17530.08620.1994-56.283138.9569-22.9881
75.32440.39730.96421.16931.47167.59980.0922-0.0985-0.6933-0.13920.0961-0.44730.43530.6036-0.17520.16050.01190.06380.15230.05070.2806-47.603937.8684-31.2388
80.63940.9796-0.94354.1516-1.11791.75820.0698-0.2318-0.10360.1887-0.2419-0.2850.07780.24810.1680.1366-0.0575-0.02640.30550.0290.1452-49.527846.7965-13.8536
93.61473.80163.66638.40274.34748.05980.1289-0.4407-0.51250.5677-0.5785-0.37180.90620.18860.33180.19190.0151-0.03070.29510.15410.2726-53.391236.5761-14.0867
101.62050.3423-1.0481.0396-0.47651.26320.1311-0.31110.11870.1147-0.08370.0269-0.21760.0523-0.04690.1425-0.0448-0.00780.3149-0.01430.1869-48.626257.0651-17.0438
117.26234.4369-7.15823.3955-5.20658.38350.1768-0.28960.22480.4353-0.12340.4717-0.7692-0.7086-0.02870.2380.019-0.00880.3732-0.06420.1835-59.291560.7535-6.6484
122.17490.4324-1.6451.2848-1.43852.28130.1443-0.2619-0.03680.1583-0.2469-0.0331-0.36730.47610.06440.1871-0.0771-0.02920.3235-0.00940.1236-50.875753.356-5.9266
132.1622-0.75840.89976.9296-3.98413.14370.1557-0.26260.08160.3832-0.233-0.0027-0.19580.20040.04580.104-0.07990.0040.289-0.01420.1678-42.695856.4534-18.1093
149.6466-7.0012.55875.2372-2.18782.0303-0.0107-0.23560.27720.5052-0.2837-0.1653-0.24030.08310.25730.1822-0.1179-0.01450.3761-0.00110.2025-42.147560.4521-14.5908
157.08070.5729-2.61832.4728-0.94754.13040.2991-0.89090.14360.4321-0.0302-0.5544-0.19330.62490.00570.1323-0.1258-0.09940.60220.15140.3138-33.593650.4911-13.2858
162.7792-0.04820.05830.84470.47911.41310.0155-0.43210.13090.0918-0.09460.096-0.21760.00020.10030.1612-0.0672-0.01780.2791-0.01770.2104-43.455963.9398-25.8482
176.0732-1.60473.48412.2466-0.06442.4174-0.2458-0.26591.24530.0855-0.0640.6748-0.705-0.25590.25480.29740.0241-0.0180.251-0.07180.471-53.951269.0988-34.9811
189.5613-6.8907-0.42175.0469-0.0782.14460.0982-0.0460.7293-0.0343-0.2388-0.8048-0.34580.20470.2270.1855-0.0468-0.01880.2550.01430.2102-42.568564.6943-33.2364
199.4005-4.03876.63047.21430.17056.3766-0.09140.21170.0143-0.5897-0.0428-0.7060.06180.3710.06640.111-0.02250.06040.21960.05060.2169-38.582252.1385-32.8669
204.220.377-4.03830.0488-0.3643.8691-0.0591-0.30350.3142-0.24770.152-0.2252-0.20060.9743-0.12140.23050.02250.05110.29030.05350.277-36.5845.3002-33.8096
211.7223-2.96361.48277.3133-1.46591.9127-0.0067-0.00340.443-0.431-0.5247-0.20030.680.27090.42170.2523-0.0250.0330.307-0.01620.1822-8.444380.2648-36.0701
226.00020.58135.53232.0680.70835.00930.0444-0.32480.0689-0.0024-0.172-0.26750.2429-0.1089-0.02020.1177-0.05850.03460.2393-0.00680.1904-9.024280.8326-27.5288
234.4318-2.997-1.87662.4466-0.27627.8998-0.07551.02330.7681-0.3104-0.28490.4291-1.6383-0.74030.25070.50820.0563-0.11170.31750.04190.4045-23.974687.9158-49.9616
242.41750.21611.30731.16270.13922.73890.0214-0.2893-0.0827-0.01230.02150.0325-0.11450.0295-0.01350.0886-0.04640.02350.1785-0.03690.0945-16.341272.8112-28.2204
250.59140.59681.27161.6367-0.66715.854-0.0761-0.1532-0.00480.0099-0.089-0.1115-0.17110.18640.17730.0893-0.0110.01980.1896-0.0190.1583-15.543272.2163-29.8498
266.0053-6.3237-1.0829.18850.4854.43010.3008-0.61920.64470.6471-0.116-0.86020.47950.6309-0.08660.2836-0.1189-0.0590.5607-0.01450.2472-8.116372.5536-10.4603
271.7543-0.81470.00395.0276-2.84122.30510.1502-0.39540.13850.2538-0.37880.0318-0.21110.14280.22390.1576-0.07990.01450.3046-0.08970.1932-13.977584.0796-22.433
287.88755.0065-3.90327.2098-6.40167.19470.01360.17220.6695-0.29350.29080.5534-0.1374-0.4381-0.2510.206-0.0148-0.04790.1943-0.07880.2148-22.942985.5932-32.2385
292.29710.29580.3822.708-0.77490.38160.0946-0.21870.07760.2551-0.1055-0.1105-0.12910.09010.02740.1861-0.10360.01370.3096-0.03240.141-21.840574.5974-17.1261
306.7594-3.98334.75495.9973-3.69889.0945-0.1219-0.80980.6051.1291-0.23480.0568-1.2452-0.50820.23410.4748-0.06180.09280.3796-0.1250.2412-22.468786.3806-8.776
310.37650.3876-1.08470.8959-1.32023.21520.2392-0.19560.10860.4555-0.1740.2198-1.20060.34220.02010.4191-0.1490.05170.3127-0.08220.2483-17.55487.6011-13.6644
321.3177-0.51760.80770.87840.43761.14530.1203-0.1988-0.15490.0883-0.05760.06490.21360.0167-0.08210.1422-0.07250.01830.30740.0040.1491-20.936266.0064-14.7354
338.6989-2.45362.29823.5042-0.38122.809-0.00580.34770.33210.2591-0.0641-0.25630.08120.25240.05430.1928-0.0779-0.0040.3781-0.01130.1266-17.35670.0874-5.8704
342.2669-1.2789-0.8836.4493.03512.82040.0583-0.1724-0.04440.1307-0.12090.2337-0.0164-0.15180.03990.0936-0.06510.02310.26770.00120.1281-29.65770.9958-18.0912
359.1021.12920.13815.43423.37325.4559-0.1126-0.2118-1.08170.397-0.2189-0.10690.14820.58550.26060.2764-0.0942-0.01680.36960.09270.2332-24.327255.9677-16.9244
366.1626-5.7821-3.26337.80143.91162.2475-0.1176-0.1446-0.06470.5128-0.22370.25950.318-0.36660.25890.2076-0.11740.04260.3448-0.04790.1592-32.392267.5551-14.4055
372.06332.98830.86695.95960.00271.3269-0.0246-0.34340.12020.2434-0.06190.2245-0.0026-0.16850.10820.1133-0.05090.01740.3812-0.01010.193-35.050667.8466-19.8425
386.5363-0.1426-4.77433.1150.62423.7062-0.0996-0.2718-1.0514-0.0879-0.3298-0.31390.50570.26630.44650.2165-0.00180.01460.25130.06170.3512-18.452255.0877-31.7751
395.3645-4.3675-2.8924.07322.04933.2537-0.02790.0345-0.182-0.41410.05660.32830.0904-0.05620.01080.1196-0.0434-0.02960.2625-0.01440.1514-30.577266.0256-33.1463
403.4503-0.34061.91764.9643.43453.7462-0.1479-0.5422-0.3670.10620.11420.35010.3273-0.9228-0.04960.17410.00720.00650.2672-0.02880.3116-34.200578.266-34.5989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:9)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 10:25)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 26:30)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 31:70)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 71:84)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 85:100)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 101:112)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 113:137)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 138:146)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 147:164)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 165:175)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 176:183)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 184:202)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 203:216)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 217:222)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 223:237)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 238:251)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 252:258)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 259:267)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 268:275)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 1:6)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 7:23)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 24:30)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 31:51)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 52:76)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 77:83)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 84:100)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 101:112)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 113:131)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 132:136)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 137:146)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 147:169)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 170:183)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 184:199)
35X-RAY DIFFRACTION35(CHAIN B AND RESID 200:207)
36X-RAY DIFFRACTION36(CHAIN B AND RESID 208:217)
37X-RAY DIFFRACTION37(CHAIN B AND RESID 218:229)
38X-RAY DIFFRACTION38(CHAIN B AND RESID 230:251)
39X-RAY DIFFRACTION39(CHAIN B AND RESID 252:267)
40X-RAY DIFFRACTION40(CHAIN B AND RESID 268:275)

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