[English] 日本語
Yorodumi
- PDB-4nek: Putative enoyl-CoA hydratase/carnithine racemase from Magnetospir... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nek
TitlePutative enoyl-CoA hydratase/carnithine racemase from Magnetospirillum magneticum AMB-1
ComponentsEnoyl-CoA hydratase/carnithine racemase
KeywordsISOMERASE / NYSGRC / New York Structural Genomics Research Consortium / PSI-Biology
Function / homology
Function and homology information


delta(3)-delta(2)-enoyl-CoA isomerase activity / peroxisome
Similarity search - Function
: / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-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 ...: / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Enoyl-CoA hydratase/carnithine racemase
Similarity search - Component
Biological speciesMagnetospirillum magneticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsTkaczuk, K.L. / Cooper, D.R. / Geffken, K. / Chapman, H.C. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. ...Tkaczuk, K.L. / Cooper, D.R. / Geffken, K. / Chapman, H.C. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Putative enoyl-CoA hydratase/carnithine racemase from Magnetospirillum magneticum AMB-1
Authors: Tkaczuk, K.L. / Cooper, D.R. / Geffken, K. / Chapman, H.C. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics ...Authors: Tkaczuk, K.L. / Cooper, D.R. / Geffken, K. / Chapman, H.C. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionOct 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enoyl-CoA hydratase/carnithine racemase
B: Enoyl-CoA hydratase/carnithine racemase
C: Enoyl-CoA hydratase/carnithine racemase
D: Enoyl-CoA hydratase/carnithine racemase
E: Enoyl-CoA hydratase/carnithine racemase
F: Enoyl-CoA hydratase/carnithine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,64511
Polymers163,1146
Non-polymers5315
Water6,954386
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Enoyl-CoA hydratase/carnithine racemase
B: Enoyl-CoA hydratase/carnithine racemase
F: Enoyl-CoA hydratase/carnithine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8766
Polymers81,5573
Non-polymers3183
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-77 kcal/mol
Surface area28470 Å2
MethodPISA
3
C: Enoyl-CoA hydratase/carnithine racemase
D: Enoyl-CoA hydratase/carnithine racemase
E: Enoyl-CoA hydratase/carnithine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7695
Polymers81,5573
Non-polymers2122
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-77 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.285, 156.683, 79.297
Angle α, β, γ (deg.)90.000, 113.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 250
2010B2 - 250
1020A2 - 251
2020C2 - 251
1030A2 - 252
2030D2 - 252
1040A2 - 252
2040E2 - 252
1050A2 - 251
2050F2 - 251
1060B1 - 250
2060C1 - 250
1070B2 - 250
2070D2 - 250
1080B2 - 250
2080E2 - 250
1090B1 - 250
2090F1 - 250
10100C2 - 251
20100D2 - 251
10110C2 - 251
20110E2 - 251
10120C1 - 252
20120F1 - 252
10130D2 - 252
20130E2 - 252
10140D2 - 251
20140F2 - 251
10150E2 - 251
20150F2 - 251

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Detailsbiological unit is the same as asym.

-
Components

#1: Protein
Enoyl-CoA hydratase/carnithine racemase


Mass: 27185.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magneticum (bacteria) / Strain: AMB-1 / Gene: amb4133 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2VZN8
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG550 30%, 0.05 M Magnesium chloride hexahydrate, HEPES 0.1M pH 7.5, 1.5 M NaCl, vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013 / Details: mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 74539 / % possible obs: 99.3 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.147 / Χ2: 0.803 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.343.40.86834780.835193.1
2.34-2.383.70.86836320.864197.1
2.38-2.434.10.89337120.852198.9
2.43-2.484.60.84137400.835199.9
2.48-2.5350.80637050.833199.9
2.53-2.595.20.74137140.848199.8
2.59-2.665.30.63138050.856199.9
2.66-2.735.30.52537060.858199.8
2.73-2.815.30.42737480.834199.8
2.81-2.95.30.33237180.833199.8
2.9-35.30.28237510.827199.8
3-3.125.30.2137360.795199.8
3.12-3.265.30.15537380.782199.8
3.26-3.445.40.11437480.768199.8
3.44-3.655.40.08537320.771199.8
3.65-3.935.40.06637460.825199.8
3.93-4.335.50.05537530.859199.8
4.33-4.955.60.05137760.953199.9
4.95-6.245.70.04337700.6351100
6.24-405.80.02638310.512199.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.154 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.221
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 3263 5 %RANDOM
Rwork0.1764 ---
obs0.178 64853 86.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.68 Å2 / Biso mean: 35.8687 Å2 / Biso min: 11.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-0.64 Å2
2--0.87 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11169 0 35 386 11590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911391
X-RAY DIFFRACTIONr_bond_other_d0.0070.0211226
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.99715415
X-RAY DIFFRACTIONr_angle_other_deg1.22325812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65651502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51723.853449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.401151714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8811584
X-RAY DIFFRACTIONr_chiral_restr0.0820.21778
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112940
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022396
X-RAY DIFFRACTIONr_mcbond_it2.523.2356026
X-RAY DIFFRACTIONr_mcbond_other2.5193.2356025
X-RAY DIFFRACTIONr_mcangle_it3.8034.8437522
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A142940.07
12B142940.07
21A143280.07
22C143280.07
31A142440.07
32D142440.07
41A144150.07
42E144150.07
51A142960.08
52F142960.08
61B145650.06
62C145650.06
71B142830.07
72D142830.07
81B142930.07
82E142930.07
91B143410.08
92F143410.08
101C142870.07
102D142870.07
111C143560.07
112E143560.07
121C144910.07
122F144910.07
131D142480.07
132E142480.07
141D142370.08
142F142370.08
151E143790.07
152F143790.07
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 106 -
Rwork0.249 2236 -
all-2342 -
obs--42.52 %

+
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://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