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- PDB-3ej9: Structural and mechanistic analysis of trans-3-chloroacrylic acid... -

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Basic information

Entry
Database: PDB / ID: 3ej9
TitleStructural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity
Components
  • Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
  • Beta-subunit of trans-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / trans-3-chloroacrylic acid dehalogenase / CaaD / dehalogenase / Isomerase
Function / homology
Function and homology information


2-hydroxymuconate tautomerase / : / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-hydroxymuconate tautomerase / 2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas pavonaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPegan, S. / Serrano, H. / Whitman, C.P. / Mesecar, A.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity.
Authors: Pegan, S.D. / Serrano, H. / Whitman, C.P. / Mesecar, A.D.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
B: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
C: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
D: Beta-subunit of trans-3-chloroacrylic acid dehalogenase
E: Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
F: Beta-subunit of trans-3-chloroacrylic acid dehalogenase


Theoretical massNumber of molelcules
Total (without water)48,0076
Polymers48,0076
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint-67 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.280, 69.670, 89.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-subunit of trans-3-chloroacrylic acid dehalogenase


Mass: 8485.717 Da / Num. of mol.: 3 / Mutation: E52Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas pavonaceae (bacteria) / Gene: caaD1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EV85
#2: Protein Beta-subunit of trans-3-chloroacrylic acid dehalogenase


Mass: 7516.571 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas pavonaceae (bacteria) / Gene: caaD2 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EV84
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 1.82 Å3/Da / Density % sol: 32.43 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→55.1 Å / Num. all: 56197 / Num. obs: 56197 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.55 Å / % possible all: 86.1

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EJ3

3ej3


Resolution: 1.5→55.05 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.815 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24704 2850 5.1 %RANDOM
Rwork0.21119 ---
obs0.21296 53285 97.41 %-
all-56135 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.789 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 0 378 3199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222956
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.9584012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5085392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.94823.407135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43715531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3431528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022206
X-RAY DIFFRACTIONr_nbd_refined0.190.21415
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22028
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.227
X-RAY DIFFRACTIONr_mcbond_it0.4751.51919
X-RAY DIFFRACTIONr_mcangle_it0.70523015
X-RAY DIFFRACTIONr_scbond_it1.26431141
X-RAY DIFFRACTIONr_scangle_it1.8964.5980
LS refinement shellResolution: 1.5→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 191 -
Rwork0.209 3389 -
obs--86.08 %
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)
136.4188-2.6632-1.55121.4994-0.82460.8964-0.0371-0.23880.20610.04670.09510.333-0.0544-0.1201-0.0581-0.1549-0.00820.0082-0.1524-0.0231-0.0621-13.56197.2138-13.4527
29.96972.5155-5.1377.5828-7.42858.0593-0.2076-0.2787-0.23970.219-0.2274-0.47060.17350.16360.435-0.15020.0089-0.0027-0.12590.0033-0.1408-0.78190.6225-10.0933
311.6783-3.4265-5.52594.69250.59877.9081-0.2888-0.2756-0.38570.32340.07680.14380.3420.08870.212-0.13480.00130.0242-0.12290.0064-0.1758-9.659-1.7429-4.514
419.5866-5.6924-1.400810.8463-3.74332.9405-0.073-0.12460.0735-0.0139-0.0210.0823-0.1039-0.03150.094-0.1140.03380.0344-0.10980.0011-0.1626-18.30217.2314-3.243
519.5646-2.7554-7.717528.74325.458418.0121-0.3248-0.3469-0.46050.28570.38950.8862-0.0443-0.7336-0.0647-0.12040.07010.0866-0.01730.0421-0.0075-25.630710.4202-4.0622
617.3399-2.0478-10.399220.613610.717522.496-0.5226-1.115-0.59041.0162-0.33460.64231.1169-0.39330.8572-0.0036-0.05450.08260.02070.03470.0054-25.91563.0243-7.588
719.6001-0.2808-3.66732.5984-0.85571.2175-0.04420.23480.0199-0.05820.03950.10180.0554-0.03990.0047-0.1743-0.0181-0.002-0.147-0.0267-0.148-10.05772.9089-15.0469
86.1995-2.7038-4.701413.34823.26266.45020.1023-0.27450.32180.1330.0776-0.6486-0.13750.2018-0.1799-0.203-0.0222-0.0472-0.12770.0254-0.07562.7812.486-15.7719
93.17232.1287-2.715419.2136-9.69819.38570.002-0.33970.00290.9305-0.292-0.7341-0.20010.25540.29-0.1473-0.0029-0.0733-0.05050.0127-0.06045.70897.5748-11.3911
104.2029-9.7469-8.33430.353920.659819.66530.15550.11690.0622-0.2559-0.11260.13170.1249-0.0119-0.0429-0.15230.0376-0.0335-0.1304-0.0001-0.132-8.540616.4969-25.615
110.036-0.63891.077111.3269-19.095632.19250.35560.29310.4550.67330.33420.7283-0.3817-0.5268-0.6898-0.05510.03930.0578-0.08580.06790.0937-13.081630.7336-24.5291
127.7795-3.8097-3.047914.4043.2133.36490.04940.24060.0868-0.4319-0.00410.612-0.105-0.1779-0.0452-0.12190.0047-0.0218-0.12860.0383-0.0415-8.237128.3193-31.2869
1316.5155-9.8056-0.67614.55083.73246.30540.21980.54920.449-0.8048-0.134-0.505-0.29860.3542-0.0858-0.0721-0.02770.0358-0.11890.0256-0.0718-0.677821.4497-33.9527
1415.07041.05465.77774.36343.367914.82650.02770.66150.0942-0.53-0.0226-0.45840.34570.3937-0.0051-0.04370.04460.09080.02220.0306-0.01682.97314.9988-36.1179
1515.57210.2349-4.23754.64661.19188.7733-0.10080.9701-0.4039-0.54820.0997-0.46890.34910.24730.0011-0.04490.03810.0194-0.0384-0.0189-0.1074-5.91713.7078-36.5998
163.0871-4.5998-7.43026.926312.021130.32970.23740.15630.40440.08350.06680.0522-0.546-0.0686-0.3042-0.14540.00230.0287-0.1306-0.0015-0.0591-13.807422.9908-21.085
1725.2802-6.89412.1765.7271-3.812610.6513-0.3071-0.03270.02660.29530.13690.0012-0.611-0.04470.1702-0.0334-0.01930.0291-0.1571-0.0445-0.0956-9.818321.3662-10.0975
1825.8908-23.63657.268135.36071.01836.2906-0.473-0.64610.77970.44090.19230.3228-0.959-0.38140.28070.1957-0.01030.0101-0.0438-0.07940.0575-9.18126.1346-4.9324
192.4135-4.00155.100628.9646-28.32331.81670.03320.02390.0703-0.04090.32290.2303-0.2377-0.5301-0.3562-0.15730.040.0371-0.1157-0.005-0.1165-15.76227.0399-28.4946
200.3175-1.22821.05189.78394.204117.08940.12370.1906-0.1182-0.3524-0.08570.02680.30950.1338-0.0381-0.0666-0.0149-0.0278-0.1299-0.0112-0.1098-11.534-7.4618-25.3734
2113.13840.41526.888410.0242-4.296712.14910.17320.5219-0.6172-0.9745-0.18540.10820.72340.41360.01220.02440.023-0.0545-0.1396-0.0274-0.1069-13.8953-7.079-34.5537
229.3231-9.05625.296812.2815-1.79599.97420.28280.23640.1158-0.5214-0.02390.62450.2389-0.3336-0.2589-0.0751-0.0222-0.0693-0.07660.0003-0.0515-20.46190.6022-35.7827
2311.2923-0.4792-1.774726.0063-2.57785.1310.0550.4251-0.0532-0.3909-0.07060.2681-0.3494-0.36350.0156-0.03030.073-0.0773-0.0034-0.018-0.0121-24.94459.3094-37.9655
2425.875-7.16739.447118.09875.64530.16040.37691.5681-0.3561-1.04910.0830.37850.02850.192-0.45990.02680.0128-0.07530.0015-0.0228-0.1039-16.50989.4514-41.7719
252.204-3.39543.65198.6526-10.181512.18750.01750.03980.02020.0289-0.131-0.1124-0.13020.11740.1135-0.1335-0.00140.0034-0.1344-0.0088-0.1474-10.87552.0381-26.906
2614.0689-4.8089-0.0764.72030.67727.9411-0.1741-0.4595-0.40260.20170.10610.59950.2356-0.52330.068-0.1215-0.02350.0408-0.14310.0022-0.0876-17.1222-3.485-11.8859
271.4271-2.7766-1.133315.591512.868718.95360.01440.1356-0.4117-0.1237-0.05550.42420.76-0.28530.0411-0.0252-0.05750.0222-0.1069-0.0044-0.036-14.9045-11.0773-17.3479
2851.0471-4.70844.95833.11560.33552.50850.06970.16-0.11540.17920.1164-0.1765-0.1894-0.0619-0.1862-0.1464-0.0120.004-0.1924-0.0227-0.051-12.437512.0011-13.5187
291.57280.55070.89127.79349.464311.52560.0241-0.27870.225-0.2849-0.25030.4886-0.8396-0.47060.22630.08170.1430.14670.02760.03230.0266-24.99719.7194-8.7957
3016.8166-9.60445.44738.1664-3.856210.82-0.2149-0.86460.47340.46890.2837-0.0725-0.821-0.6619-0.06890.00480.03750.0974-0.0412-0.0196-0.052-18.121819.3216-3.3158
3119.6817-9.5544.575621.8329-2.52245.74840.0439-0.98210.03550.58940.2497-0.0089-0.0628-0.0871-0.2936-0.0953-0.0340.0119-0.0581-0.0097-0.1364-10.459311.7433-1.4642
3211.42386.97481.172811.142-4.076.32590.2179-0.4425-0.57110.4986-0.166-0.2732-0.26150.0824-0.05190.0296-0.0211-0.0777-0.0332-0.0027-0.056-4.3019.2151-1.3504
3321.1935-2.48549.6655.3457-3.135610.5764-0.0519-0.2456-0.02610.2362-0.0247-0.3286-0.17120.46620.0766-0.1204-0.0119-0.0051-0.1406-0.0234-0.1003-5.682115.3583-8.943
3432.41618.550520.50963.00366.550614.7154-0.0615-0.4470.40510.1983-0.19110.3949-0.2124-0.71560.2526-0.14460.04020.0277-0.06510.0016-0.0346-23.725616.0249-15.8626
357.9258-7.14022.015426.1006-5.21075.50580.10480.1016-0.11980.4147-0.24040.7264-0.1103-0.17750.1356-0.1695-0.02340.05850.0082-0.00420.0118-27.60217.0477-19.1284
369.3319-11.9525-4.953424.16256.442711.28320.5447-0.0027-0.0384-0.54-0.31851.3229-0.6491-0.3809-0.2262-0.0553-0.08810.05090.15860.02970.2719-33.22524.7591-18.85
372.0787-4.7799-2.625718.915511.00317.7599-0.0209-0.05930.0957-0.11880.0532-0.2351-0.20130.1502-0.0322-0.14860.0113-0.0033-0.12410.004-0.1186-3.339910.4214-24.987
387.83929.39973.524217.8648.84837.61090.01870.2592-0.7216-0.14370.1799-1.2008-0.04580.6249-0.1986-0.11880.01650.0808-0.07840.03460.04678.71098.247-27.7079
391.9251-3.4297-0.663716.4997-2.86053.12350.10530.0340.04740.2316-0.1688-0.0935-0.07630.06070.0635-0.191-0.02730.0136-0.12080.042-0.05235.433315.894-24.4729
4030.5223-9.65073.182323.9573.53295.289-0.07420.05310.4778-0.15780.1041-0.252-0.0230.2024-0.0298-0.1315-0.02080.0388-0.12540.0497-0.08561.045725.0748-23.9088
418.9167-7.41647.436115.3808-6.166811.8047-0.02110.00610.11560.3628-0.258-0.2825-0.45280.26370.2791-0.0941-0.0580.0046-0.10930.02380.054-0.698528.1452-19.2406
422.9451-0.4301-0.485324.5737.93326.9677-0.0522-0.20510.26910.49040.2106-0.4026-0.3040.2728-0.1584-0.1453-0.0033-0.0248-0.13630.0071-0.1136-1.362617.5499-17.0223
432.85052.22033.43353.56463.15536.83080.32160.0598-0.120.0079-0.1043-0.27440.3037-0.1051-0.2173-0.10750.02410.0059-0.146-0.0097-0.1382-4.79961.5932-27.9565
4411.99110.86997.56813.9141.619313.1990.04030.55490.2028-1.254-0.07890.282-0.1170.03970.0385-0.05140.04790.0067-0.1067-0.0225-0.1368-9.60934.5813-38.4253
4524.71226.3934.15548.65310.95235.21650.4364-0.2137-0.5217-0.1169-0.1795-1.27250.10160.9063-0.2569-0.00070.04570.04390.0789-0.03490.02671.75381.0451-34.7485
467.4654-8.75721.142239.5536-22.056522.9118-0.1585-0.3202-0.2498-0.08050.15250.16320.1469-0.37310.0059-0.19790.02290.0485-0.10440.0041-0.0829-19.15634.9087-23.586
471.37372.84521.760410.96-4.645615.8241-0.28260.18460.4775-0.0873-0.0430.9007-0.5602-0.67530.3256-0.09150.0754-0.0312-0.061-0.03190.0222-23.88116.3339-30.9234
4825.234812.0485-12.553274.6608-2.83566.38940.19430.31171.06960.09840.64742.95530.1061-2.0392-0.8417-0.21720.1422-0.09340.25320.10250.2816-33.264112.1446-30.0799
497.959-4.3784-1.378314.39421.31056.3332-0.08960.3041-0.1366-0.89310.27791.24920.3166-0.8777-0.1884-0.0357-0.0994-0.09490.11480.03450.0921-29.13182.3664-29.3814
502.77091.0918-5.82196.36461.077914.1485-0.54340.1145-0.7893-0.4718-0.1856-0.02241.4393-0.6820.7290.1464-0.1070.04380.0111-0.02430.1831-24.1487-6.958-26.7392
515.90460.64571.112215.44447.48926.82760.2493-0.1698-0.60580.223-0.24480.3921.0968-0.3938-0.0045-0.084-0.06520.0217-0.04480.02750.0129-24.4551-1.3927-19.7984
525.2727.7715-5.578223.7511-14.67419.28720.02870.28870.3494-0.13850.1370.7904-0.0956-0.3977-0.1657-0.09610.048-0.0099-0.0923-0.0211-0.043-21.616716.5156-27.7304
5310.6508-4.731-5.203712.37816.02439.93170.21580.4310.2343-0.1758-0.1105-0.0123-0.1251-0.324-0.1053-0.07370.0268-0.0576-0.05890.0248-0.1246-12.537918.6995-34.9802
549.3926-2.64156.819628.5611-12.674110.6506-0.44660.05620.5987-0.87530.7820.5643-0.961-1.0945-0.33530.11360.0663-0.00040.09420.07060.019-12.95721.9984-40.0575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 8
2X-RAY DIFFRACTION2A9 - 13
3X-RAY DIFFRACTION3A14 - 22
4X-RAY DIFFRACTION4A23 - 28
5X-RAY DIFFRACTION5A29 - 34
6X-RAY DIFFRACTION6A35 - 39
7X-RAY DIFFRACTION7A40 - 47
8X-RAY DIFFRACTION8A48 - 54
9X-RAY DIFFRACTION9A55 - 62
10X-RAY DIFFRACTION10B2 - 8
11X-RAY DIFFRACTION11B9 - 14
12X-RAY DIFFRACTION12B15 - 21
13X-RAY DIFFRACTION13B22 - 29
14X-RAY DIFFRACTION14B30 - 36
15X-RAY DIFFRACTION15B37 - 41
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