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- PDB-2xlc: Acetyl xylan esterase from Bacillus pumilus CECT5072 bound to paraoxon -

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Basic information

Entry
Database: PDB / ID: 2xlc
TitleAcetyl xylan esterase from Bacillus pumilus CECT5072 bound to paraoxon
ComponentsACETYL XYLAN ESTERASE
KeywordsHYDROLASE / CE-7 FAMILY / IRREVERSIBLE INHIBITION
Function / homology
Function and homology information


acetylesterase / polysaccharide metabolic process / acetylesterase activity
Similarity search - Function
Acetyl xylan esterase / Carbohydrate esterase 7 family / Acetyl xylan esterase (AXE1) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIETHYL PHOSPHONATE / Acetyl xylan esterase
Similarity search - Component
Biological speciesBACILLUS PUMILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGil-Ortiz, F. / Montoro-Garcia, S. / Polo, L.M. / Rubio, V. / Sanchez-Ferrer, A.
CitationJournal: Biochem.J. / Year: 2011
Title: The Crystal Structure of the Cephalosporin Deacetylating Enzyme Acetyl Xylan Esterase Bound to Paraoxon Explains the Low Sensitivity of This Serine Hydrolase to Organophosphate Inactivation.
Authors: Montoro-Garcia, S. / Gil-Ortiz, F. / Garcia-Carmona, F. / Polo, L.M. / Rubio, V. / Sanchez-Ferrer, A.
History
DepositionJul 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_conn / 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_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: ACETYL XYLAN ESTERASE
B: ACETYL XYLAN ESTERASE
C: ACETYL XYLAN ESTERASE
D: ACETYL XYLAN ESTERASE
E: ACETYL XYLAN ESTERASE
F: ACETYL XYLAN ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,88912
Polymers218,0606
Non-polymers8296
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17170 Å2
ΔGint-4.2 kcal/mol
Surface area60260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.049, 116.052, 100.248
Angle α, β, γ (deg.)90.00, 105.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A7 - 318
2113B7 - 318
3113C7 - 318
4113D7 - 318
5113E7 - 318
6113F7 - 318

NCS oper:
IDCodeMatrixVector
1given(0.3575, -0.6692, -0.6515), (-0.6644, -0.6725, 0.3261), (-0.6563, 0.3162, -0.685)13.82, -10.17, 39.55
2given(-0.9739, 0.01226, -0.2267), (-0.0279, -0.9974, 0.06591), (-0.2253, 0.07051, 0.9717)0.5586, -2.114, 0.3172
3given(0.02055, -0.5161, 0.8563), (-0.5092, -0.7425, -0.4353), (0.8604, -0.427, -0.278)-23.2, 9.63, 33.47
4given(0.4026, -0.639, -0.6554), (-0.654, -0.7018, 0.2825), (-0.6404, 0.3149, -0.7005)14.33, -8.134, 40.52
5given(-0.9719, -0.009972, -0.2352), (-0.008179, -0.9971, 0.07608), (-0.2352, 0.07587, 0.969)0.9026, -1.774, 0.18

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Components

#1: Protein
ACETYL XYLAN ESTERASE / CEPHALOSPORIN C DEACETYLASE


Mass: 36343.340 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS PUMILUS (bacteria) / Strain: CECT5072 / Plasmid: PET28A6HIS-AXE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (DE3) PLYS / References: UniProt: Q9K5F2, acetylxylan esterase
#2: Chemical
ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H11O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDIETHYL PHOSPHATE (DEP): COVALENTLY LINKED TO RESIDUE SER181
Sequence detailsSEQUENCE CONFLICTS ARE DUE TO SEQUENCES COMING FROM DIFFERENT BACILLUS PUMILUS STRAINS, PS213 ...SEQUENCE CONFLICTS ARE DUE TO SEQUENCES COMING FROM DIFFERENT BACILLUS PUMILUS STRAINS, PS213 (UNIPROT SEQUENCE) AND CECT 5072 (PDB ENTRY 2XLC)

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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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 5.5
Details: 0.2 M NH4 ACETATE, 0.1 M BIS-TRIS PH 5.5, 45% 2-METHYL-2,4-PENTANEDIOL (MPD)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.907
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.907 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 46958 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 54.137 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ODS
Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.912 / SU B: 30.858 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23608 2507 5.1 %RANDOM
Rwork0.21631 ---
obs0.21731 46958 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.763 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å20 Å20.73 Å2
2---0.02 Å20 Å2
3----3.49 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14506 0 48 40 14594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02214969
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6351.94820437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.89251862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92423.657689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.392152112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4361566
X-RAY DIFFRACTIONr_chiral_restr0.0470.22222
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111732
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_it0.1621.59292
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.314214854
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.42435677
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6974.55583
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
1A1180tight positional0.010.05
2B1180tight positional0.010.05
3C1180tight positional0.010.05
4D1180tight positional0.010.05
5E1180tight positional0.010.05
6F1180tight positional0.010.05
1A1123loose positional0.015
2B1123loose positional0.035
3C1123loose positional0.015
4D1123loose positional0.015
5E1123loose positional0.015
6F1123loose positional0.015
1A1180tight thermal0.020.5
2B1180tight thermal0.020.5
3C1180tight thermal0.020.5
4D1180tight thermal0.010.5
5E1180tight thermal0.020.5
6F1180tight thermal0.020.5
1A1123loose thermal0.0210
2B1123loose thermal0.0210
3C1123loose thermal0.0210
4D1123loose thermal0.0210
5E1123loose thermal0.0210
6F1123loose thermal0.0210
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 187 -
Rwork0.309 3385 -
obs--99.22 %
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)
10.8365-0.636-0.10751.82460.45860.76560.0025-0.1548-0.01420.08620.0946-0.12180.03540.0959-0.09720.1928-0.06210.06980.15950.00230.0631-24.4422-4.225953.5746
23.3837-1.0480.99772.9827-0.2153.16230.12040.1610.26230.1491-0.05850.0356-0.18480.0313-0.06180.2882-0.10880.10310.159-0.00830.056-28.28559.946956.0819
33.3175-1.78730.31111.1158-0.23070.73680.244-0.05580.0230.0636-0.0761-0.0241-0.09790.0159-0.1680.3136-0.0960.00590.1259-0.01020.1216-19.57636.126349.2155
41.5174-0.4698-0.20720.88690.43171.1593-0.06460.013-0.12450.04520.0077-0.039-0.0043-0.03350.05690.2716-0.080.02870.1620.0140.1069-22.7173-4.418850.7361
51.07590.02120.29170.5870.20540.77890.0935-0.1059-0.111-0.0145-0.0524-0.00310.08160.0299-0.04110.2353-0.0484-0.00090.12920.01620.1482-23.0727-9.347841.5505
62.33780.1845-0.58930.7936-0.78062.2502-0.08050.27580.1654-0.0060.0280.0909-0.1183-0.24410.05250.15310.01710.03130.0567-0.00770.0999-27.188826.092417.7038
71.9710.8693-2.55060.7133-0.01817.89470.01860.24680.04010.0550.0897-0.0081-0.013-0.748-0.10830.25190.04640.07550.14920.00060.2372-39.372720.219422.7392
81.78930.1959-1.78640.8888-0.4761.8753-0.1234-0.0602-0.1382-0.00710.05010.17580.13550.04280.07330.22170.02250.04740.18530.01830.1945-29.339614.75520.6313
91.13220.0542-0.80141.18310.67661.54780.01920.09470.0130.1255-0.00130.02420.0903-0.0778-0.01790.2275-0.00220.05930.09530.02050.1634-24.411424.435618.3149
100.48590.08570.68570.48380.01571.12340.0193-0.00940.05370.0739-0.0108-0.0038-0.05410.088-0.00850.2821-0.02960.05890.1122-0.00360.1701-15.132224.886123.0835
112.42570.48240.01381.42981.00772.2741-0.0651-0.1655-0.30460.04980.0259-0.2370.1380.36970.03920.16830.1037-0.00320.20980.13350.173723.7552-26.066525.6376
121.57691.6658-0.65043.15041.84744.88930.1745-0.3859-0.23370.12770.1023-0.4442-0.17841.1238-0.27680.13530.0917-0.0160.6020.11820.276233.9996-19.685432.7331
130.22750.18160.22651.2864-0.06781.6253-0.1114-0.1631-0.02350.1461-0.072-0.1406-0.08920.40.18350.13660.0695-0.0340.41240.08280.256524.6425-14.651728.0328
141.08040.58010.33970.32690.07942.0019-0.0648-0.1394-0.0016-0.0074-0.1063-0.02380.25270.38820.17110.19710.09350.0050.23940.12210.250320.3846-24.496925.2464
150.6137-0.1356-0.23810.48670.1540.8187-0.0992-0.2083-0.09490.05060.0029-0.03620.09280.12190.09630.17560.02640.01920.18820.05550.2310.3407-25.029727.685
161.7244-1.188-0.74942.2972-1.08332.30350.0161-0.40080.02440.43690.1351-0.0078-0.39780.4714-0.15120.3247-0.1608-0.120.3259-0.0110.117512.5396.247757.8477
171.2824-0.4457-0.16481.15380.93810.90820.0443-0.0161-0.04420.26530.0038-0.06390.23750.2405-0.04820.2952-0.0789-0.12210.49610.09150.164615.6567-7.359562.0563
180.2226-0.3675-0.36421.03440.54220.62240.078-0.1593-0.02260.0451-0.10850.0371-0.06850.3350.03040.3119-0.1104-0.04480.4810.01310.18128.8608-4.2353.129
190.8111-0.1438-0.58680.5308-0.00470.49870.0485-0.1947-0.00890.2265-0.07770.0264-0.12540.29130.02920.3515-0.1651-0.0720.4-0.00230.165311.61096.435954.5483
201.22010.0423-0.70910.33530.21850.86590.1067-0.16750.1010.0877-0.0372-0.1196-0.17310.3276-0.06950.3275-0.1297-0.05170.33480.0020.161313.80310.777245.2712
212.45230.9567-1.35361.7746-1.29211.82280.02760.35630.0115-0.0940.22840.1673-0.1278-0.4383-0.25610.20230.06070.00530.20830.00220.0856-22.509-4.2196-6.2189
223.5609-1.752-1.23472.5686-0.19950.9019-0.06790.27530.1518-0.07930.16060.0631-0.105-0.2879-0.09260.36330.062-0.04780.169-0.00130.0899-15.22054.3044-15.3524
231.4586-0.288-1.54860.57220.68931.95230.0930.07610.0718-0.0378-0.0530.0819-0.2019-0.0967-0.040.30.06170.0380.20640.03460.1094-14.21474.0438-3.7093
240.921-0.3418-1.43591.17180.0842.50950.07310.1311-0.03140.0522-0.00670.1304-0.2189-0.3353-0.06640.16790.06030.00430.2310.02370.1519-20.8494-4.844-3.1051
250.999-0.3247-0.4070.53320.13540.68790.01740.1413-0.03240.03660.00490.0303-0.0075-0.2423-0.02230.1390.00420.01330.16010.01730.1815-16.6257-12.01413.0216
261.9694-0.10380.60462.84282.23343.4450.1398-0.03950.0810.1660.0826-0.2988-0.05760.3947-0.22230.212-0.07010.06310.093-0.01040.081423.99442.3941-0.7695
275.21161.18393.19430.36280.18875.52860.01220.2855-0.4411-0.01950.0521-0.14190.08190.0061-0.06430.1598-0.0230.0940.1345-0.03620.102919.2764-7.1205-10.7821
281.37590.63441.4620.37161.01053.0095-0.0561-0.011-0.23610.00580.0003-0.04840.03870.03010.05580.1457-0.01410.00210.1094-0.00250.221315.5585-5.980.2351
290.9570.07660.03121.59790.36382.68810.1022-0.16620.1208-0.0078-0.0224-0.0603-0.35610.2592-0.07990.0834-0.07020.03390.1365-0.00090.177721.95632.97661.7082
301.2922-0.54190.53160.8631-0.52111.05070.0215-0.13210.11530.01110.0021-0.1223-0.33280.1273-0.02360.2302-0.05710.02580.1269-0.04210.189816.425110.50426.2823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 56
2X-RAY DIFFRACTION2A57 - 87
3X-RAY DIFFRACTION3A88 - 136
4X-RAY DIFFRACTION4A137 - 222
5X-RAY DIFFRACTION5A223 - 317
6X-RAY DIFFRACTION6B7 - 56
7X-RAY DIFFRACTION7B57 - 87
8X-RAY DIFFRACTION8B88 - 136
9X-RAY DIFFRACTION9B137 - 222
10X-RAY DIFFRACTION10B223 - 317
11X-RAY DIFFRACTION11C7 - 56
12X-RAY DIFFRACTION12C57 - 87
13X-RAY DIFFRACTION13C88 - 136
14X-RAY DIFFRACTION14C137 - 222
15X-RAY DIFFRACTION15C223 - 317
16X-RAY DIFFRACTION16D7 - 56
17X-RAY DIFFRACTION17D57 - 87
18X-RAY DIFFRACTION18D88 - 136
19X-RAY DIFFRACTION19D137 - 222
20X-RAY DIFFRACTION20D223 - 317
21X-RAY DIFFRACTION21E7 - 56
22X-RAY DIFFRACTION22E57 - 87
23X-RAY DIFFRACTION23E88 - 136
24X-RAY DIFFRACTION24E137 - 222
25X-RAY DIFFRACTION25E223 - 318
26X-RAY DIFFRACTION26F7 - 56
27X-RAY DIFFRACTION27F57 - 87
28X-RAY DIFFRACTION28F88 - 136
29X-RAY DIFFRACTION29F137 - 222
30X-RAY DIFFRACTION30F223 - 318

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