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- PDB-6c7c: Crystal structure of Enoyl-CoA hydratase, EchA3, from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 6c7c
TitleCrystal structure of Enoyl-CoA hydratase, EchA3, from Mycobacterium ulcerans Agy99
ComponentsEnoyl-CoA hydratase, EchA3
KeywordsLYASE / SSGCID / enoyl-CoA hydratase / EchA3 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyEnoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta / Enoyl-CoA hydratase, EchA3
Function and homology information
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Enoyl-CoA hydratase, EchA3, from Mycobacterium ulcerans Agy99
Authors: Abendroth, J. / Mayclin, S.J. / Sankaran, B. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase, EchA3
B: Enoyl-CoA hydratase, EchA3
C: Enoyl-CoA hydratase, EchA3


Theoretical massNumber of molelcules
Total (without water)74,2933
Polymers74,2933
Non-polymers00
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-12 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.650, 75.520, 82.700
Angle α, β, γ (deg.)90.000, 115.430, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 16 or resid 18...
21(chain B and (resid 3 through 10 or (resid 11...
31(chain C and (resid 3 through 10 or (resid 11...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYILEILE(chain A and (resid 3 through 16 or resid 18...AA3 - 167 - 20
12METMETASNASN(chain A and (resid 3 through 16 or resid 18...AA18 - 2422 - 28
13LEULEUASNASN(chain A and (resid 3 through 16 or resid 18...AA26 - 5430 - 58
14HISHISHISHIS(chain A and (resid 3 through 16 or resid 18...AA5559
15METMETLEULEU(chain A and (resid 3 through 16 or resid 18...AA1 - 2315 - 235
16METMETLEULEU(chain A and (resid 3 through 16 or resid 18...AA1 - 2315 - 235
17METMETLEULEU(chain A and (resid 3 through 16 or resid 18...AA1 - 2315 - 235
18METMETLEULEU(chain A and (resid 3 through 16 or resid 18...AA1 - 2315 - 235
21GLYGLYASPASP(chain B and (resid 3 through 10 or (resid 11...BB3 - 107 - 14
22ASPASPALAALA(chain B and (resid 3 through 10 or (resid 11...BB11 - 1215 - 16
23GLYGLYGLYGLY(chain B and (resid 3 through 10 or (resid 11...BB3 - 2307 - 234
24GLYGLYGLYGLY(chain B and (resid 3 through 10 or (resid 11...BB3 - 2307 - 234
25GLYGLYGLYGLY(chain B and (resid 3 through 10 or (resid 11...BB3 - 2307 - 234
26GLYGLYGLYGLY(chain B and (resid 3 through 10 or (resid 11...BB3 - 2307 - 234
31GLYGLYASPASP(chain C and (resid 3 through 10 or (resid 11...CC3 - 107 - 14
32ASPASPALAALA(chain C and (resid 3 through 10 or (resid 11...CC11 - 1215 - 16
33METMETGLYGLY(chain C and (resid 3 through 10 or (resid 11...CC1 - 2305 - 234
34METMETGLYGLY(chain C and (resid 3 through 10 or (resid 11...CC1 - 2305 - 234
35METMETGLYGLY(chain C and (resid 3 through 10 or (resid 11...CC1 - 2305 - 234
36METMETGLYGLY(chain C and (resid 3 through 10 or (resid 11...CC1 - 2305 - 234

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Components

#1: Protein Enoyl-CoA hydratase, EchA3


Mass: 24764.260 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Strain: Agy99 / Gene: echA3, MUL_0713 / Plasmid: MyulA.00829.b.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0PLZ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Qiagen JCSG core 1 screen B2: 20% PEG 8000, 100mM HEPES free acid/NaOH pH 7.5: MyulA.00829.a.A1.PS00793 at 20.8mg/ml: cryo: 20% EG: tray 230568 b2: puck lwt7-11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→19.665 Å / Num. obs: 41269 / % possible obs: 96.8 % / Redundancy: 3.646 % / Biso Wilson estimate: 20.81 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.072 / Χ2: 0.985 / Net I/σ(I): 14.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.152.860.165627970.9740.289.2
2.15-2.213.3320.147.4929200.9840.16795.9
2.21-2.283.4380.1379.4127330.980.16391.8
2.28-2.353.8030.1319.1727900.9850.15396.7
2.35-2.423.8450.11210.1927420.990.1397.9
2.42-2.513.780.10310.926510.9890.12197.6
2.51-2.63.8090.0911.9325430.9920.10597.4
2.6-2.713.7040.08612.8824490.9910.10198.4
2.71-2.833.7940.07714.3323760.9930.0998.5
2.83-2.973.7660.06915.4423000.9930.08198
2.97-3.133.7680.06217.1221590.9940.07298.2
3.13-3.323.7280.05818.6120470.9930.06798.9
3.32-3.553.6790.05620.2219390.9940.06598.8
3.55-3.833.6680.05321.3618150.9930.06398.2
3.83-4.23.6420.04922.1316660.9940.05799.1
4.2-4.73.7460.04822.9515230.9950.05699.4
4.7-5.423.7270.0522.0713340.9940.05999.5
5.42-6.643.7550.04521.8511410.9960.05399
6.64-9.393.8650.03723.719040.9970.04399.1
9.39-19.6653.7910.03224.664400.9980.03787.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r6h

3r6h


Resolution: 2.1→19.665 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.53
RfactorNum. reflection% reflection
Rfree0.2243 2028 4.91 %
Rwork0.1743 --
obs0.1767 41262 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.16 Å2 / Biso mean: 29.41 Å2 / Biso min: 10.57 Å2
Refinement stepCycle: final / Resolution: 2.1→19.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5062 0 0 494 5556
Biso mean---33.94 -
Num. residues----689
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2871X-RAY DIFFRACTION6.332TORSIONAL
12B2871X-RAY DIFFRACTION6.332TORSIONAL
13C2871X-RAY DIFFRACTION6.332TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15250.27261590.20332521268089
2.1525-2.21060.2631430.20662754289796
2.2106-2.27550.32841370.26012630276792
2.2755-2.34890.271380.21592794293297
2.3489-2.43270.24151500.19562809295998
2.4327-2.52990.26351310.19352823295498
2.5299-2.64480.26431490.19232788293798
2.6448-2.78380.25481640.19252848301298
2.7838-2.95770.26041220.19092840296298
2.9577-3.18520.21661290.17782859298898
3.1852-3.50410.21111460.16552845299199
3.5041-4.00740.19381660.15252864303099
4.0074-5.03490.161390.134829193058100
5.0349-19.66620.20021550.150229403095100
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)
11.03840.00790.38412.0922-0.31510.9757-0.10310.1487-0.0641-0.13990.0202-0.15710.15040.1490.07910.1897-0.00730.05150.1819-0.00120.261524.851-5.726221.1899
25.04422.23220.89981.89331.36251.1876-0.1192-0.3959-0.36750.3669-0.0920.17010.6890.0993-0.13550.50170.0230.19850.06970.01370.391117.0452-23.749327.5311
37.22191.1284-2.63753.0459-0.45423.2751-0.12610.45570.3939-0.2740.1154-0.0588-0.0349-0.11220.03260.3031-0.0595-0.00560.2962-0.02140.200816.7211-11.41566.3787
40.9567-0.33180.52871.81390.31611.1514-0.00920.0450.257-0.19330.0127-0.0927-0.35150.1606-0.00420.2664-0.0920.02040.1779-0.01930.316124.700327.995322.1908
56.9197-4.0519-0.18738.46590.14355.17890.09970.50220.1569-0.2866-0.11520.558-0.6656-0.4595-0.00310.2566-0.015-0.03260.2120.00760.258511.390427.258713.0162
61.1707-0.21-0.22990.46180.01120.4684-0.01590.00360.0043-0.0166-0.00240.025-0.09020.0280.01720.1802-0.0407-0.00330.1609-0.00320.231213.201514.044924.6006
71.9225-1.3001-1.09011.63410.48271.9855-0.0355-0.11680.1228-0.05740.0943-0.34640.10480.4329-0.03040.1503-0.07320.00930.18890.02520.296731.091712.033622.2096
82.7199-4.58021.80738.0641-2.30444.87360.0440.3932-0.6059-0.17420.06851.0683-0.5568-0.4407-0.22610.3292-0.0384-0.03850.32320.02970.292110.96617.34527.3698
92.0832-0.8242-0.07332.4570.59343.46260.0508-0.07760.21330.1909-0.15040.82530.0316-0.28490.07110.1417-0.00170.00680.24520.01970.3721-22.16491.058730.257
100.72040.9628-0.52724.2976-0.14330.6415-0.02660.175-0.0501-0.14690.02840.25440.0449-0.1112-0.00790.1233-0.03730.00530.2478-0.02060.2766-18.6495-3.334124.7797
111.8799-0.0916-0.27092.87020.35161.955-0.25730.1979-0.3309-0.32280.16070.25860.295-0.02980.06910.172-0.06510.02750.2221-0.0260.2824-12.5352-8.718320.0588
121.4822-1.0268-0.58633.1051-0.52320.6308-0.09860.0472-0.2148-0.08050.00190.11540.1005-0.06240.09810.1117-0.0376-0.00510.1613-0.01640.2287-4.5502-3.956827.6336
131.5773-1.89910.20242.70030.17521.6519-0.02020.2253-0.242-0.26740.09060.22040.2444-0.1124-0.05250.2192-0.07820.03550.2392-0.03080.28430.565-10.920215.8354
141.6794-0.8571-1.33011.59780.29991.6068-0.1415-0.1192-0.1418-0.03490.0846-0.02720.04490.12570.06550.1402-0.00240.00220.1965-0.00720.24665.9391-6.931827.7041
152.4878-2.22142.24384.4732-5.82327.8486-0.0312-0.46150.13450.63080.20310.2221-0.5107-0.1647-0.16870.16580.0280.00380.198-0.05380.2564-7.97156.73336.3143
163.91510.7034-1.24542.07881.29055.6588-0.1150.46560.1946-0.20640.09510.32590.2147-0.26950.03860.173-0.0547-0.05580.19490.01780.1568-4.734614.808218.2748
174.14311.5342.21947.65515.98578.64480.09130.5494-0.3734-0.3243-0.0646-0.03460.2607-0.2942-0.00710.2565-0.083-0.00310.4183-0.05220.2123-5.0188-5.61837.905
183.3492.68990.93512.93780.3360.5292-0.00370.2641-0.27750.01720.0499-0.1990.34870.297-0.07820.39340.05640.16340.1954-0.00930.434829.1916-25.951215.5374
191.9388-0.0574-0.13860.9658-0.31883.2448-0.03420.265-0.0929-0.2434-0.0684-0.3564-0.04660.46030.16340.33020.01230.14530.2556-0.00180.301728.5311-16.278612.3523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 101 through 180 )B101 - 180
2X-RAY DIFFRACTION2chain 'B' and (resid 181 through 199 )B181 - 199
3X-RAY DIFFRACTION3chain 'B' and (resid 200 through 230 )B200 - 230
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 63 )C1 - 63
5X-RAY DIFFRACTION5chain 'C' and (resid 64 through 90 )C64 - 90
6X-RAY DIFFRACTION6chain 'C' and (resid 91 through 180 )C91 - 180
7X-RAY DIFFRACTION7chain 'C' and (resid 181 through 209 )C181 - 209
8X-RAY DIFFRACTION8chain 'C' and (resid 210 through 230 )C210 - 230
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 12 )A1 - 12
10X-RAY DIFFRACTION10chain 'A' and (resid 13 through 44 )A13 - 44
11X-RAY DIFFRACTION11chain 'A' and (resid 45 through 90 )A45 - 90
12X-RAY DIFFRACTION12chain 'A' and (resid 91 through 129 )A91 - 129
13X-RAY DIFFRACTION13chain 'A' and (resid 130 through 148 )A130 - 148
14X-RAY DIFFRACTION14chain 'A' and (resid 149 through 180 )A149 - 180
15X-RAY DIFFRACTION15chain 'A' and (resid 181 through 197 )A181 - 197
16X-RAY DIFFRACTION16chain 'A' and (resid 198 through 209 )A198 - 209
17X-RAY DIFFRACTION17chain 'A' and (resid 210 through 231 )A210 - 231
18X-RAY DIFFRACTION18chain 'B' and (resid 3 through 44 )B3 - 44
19X-RAY DIFFRACTION19chain 'B' and (resid 45 through 100 )B45 - 100

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