[English] 日本語
Yorodumi
- PDB-6c7c: Crystal structure of Enoyl-CoA hydratase, EchA3, from Mycobacteri... -

+
Open data


ID or keywords:

Loading...

-
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 / catalytic activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more