[English] 日本語
Yorodumi
- PDB-4jwv: Crystal Structure of putative short chain enoyl-CoA hydratase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jwv
TitleCrystal Structure of putative short chain enoyl-CoA hydratase from Novosphingobium aromaticivorans DSM 12444
ComponentsShort chain enoyl-CoA hydratase
KeywordsLYASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / PFAM PF00378
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity
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, conserved site / Enoyl-CoA hydratase/isomerase signature. / 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 ...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, conserved site / Enoyl-CoA hydratase/isomerase signature. / 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
Short chain enoyl-CoA hydratase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCooper, D.R. / Mikolajczak, K. / Cymborowski, M. / Grabowski, M. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. ...Cooper, D.R. / Mikolajczak, K. / Cymborowski, M. / Grabowski, M. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of putative short chain enoyl-CoA hydratase from Novosphingobium aromaticivorans DSM 12444
Authors: Cooper, D.R. / Mikolajczak, K. / Cymborowski, M. / Grabowski, M. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. / Almo, S.C. / Minor, W.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_ref_seq_dif
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_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Short chain enoyl-CoA hydratase
B: Short chain enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)60,6372
Polymers60,6372
Non-polymers00
Water6,269348
1
A: Short chain enoyl-CoA hydratase
B: Short chain enoyl-CoA hydratase

A: Short chain enoyl-CoA hydratase
B: Short chain enoyl-CoA hydratase

A: Short chain enoyl-CoA hydratase
B: Short chain enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)181,9106
Polymers181,9106
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area23290 Å2
ΔGint-130 kcal/mol
Surface area53590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.311, 116.311, 116.311
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-412-

HOH

31B-334-

HOH

41B-357-

HOH

51B-439-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 256
2010B3 - 256
DetailsEach monomer in the ASU is 1/3 of a trimer that is 1/2 of a hexamer.

-
Components

#1: Protein Short chain enoyl-CoA hydratase


Mass: 30318.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_1463 / Plasmid: pSGC-His_L-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q2G8B7, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: The drop was 200 nl 13.75 mg/ml protein mixed with 200 nl Qiagen Cryos Suite condition A4 (4.25 % isopropanol, 1.7 M Ammonium Sulfate, 15% glycerol). The crystallization reservoir contained ...Details: The drop was 200 nl 13.75 mg/ml protein mixed with 200 nl Qiagen Cryos Suite condition A4 (4.25 % isopropanol, 1.7 M Ammonium Sulfate, 15% glycerol). The crystallization reservoir contained only 1.5 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionRedundancy: 11.1 % / Av σ(I) over netI: 35.66 / Number: 458154 / Rmerge(I) obs: 0.098 / Χ2: 0.92 / D res high: 1.9 Å / D res low: 40 Å / Num. obs: 41251 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.154099.810.0320.54411.6
4.095.1510010.0651.35112.3
3.584.0910010.0711.42112.4
3.253.5810010.0650.98912.4
3.023.2510010.0730.89612.5
2.843.0210010.0950.91912.5
2.72.8410010.1210.90112.5
2.582.710010.1510.89412.5
2.482.5810010.1960.90112.5
2.392.4810010.2350.87912.5
2.322.3910010.2780.8912.5
2.252.3210010.3590.86712.5
2.192.2510010.4350.86112.5
2.142.1910010.5480.83912.4
2.092.1410010.6420.85812.3
2.052.0910010.7910.86810.1
2.012.0597.810.8810.8158.3
1.972.0197.410.7926.9
1.931.9797.610.7955.7
1.91.9397.710.8284.8
ReflectionResolution: 2.1→40 Å / Num. obs: 30946 / % possible obs: 100 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.116 / Χ2: 1.721 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.14120.77315250.5011100
2.14-2.1812.20.71315180.5091100
2.18-2.2212.40.63415170.5161100
2.22-2.2612.40.53815480.551100
2.26-2.3112.50.45815310.5731100
2.31-2.3712.50.38215210.6051100
2.37-2.4212.50.33615660.651100
2.42-2.4912.50.28815170.6961100
2.49-2.5612.50.2515120.7321100
2.56-2.6512.50.20715560.8271100
2.65-2.7412.60.17915410.9341100
2.74-2.8512.50.1515321.1121100
2.85-2.9812.50.13315511.381100
2.98-3.1412.50.10515571.6181100
3.14-3.3312.40.09615322.0931100
3.33-3.5912.30.08515412.7521100
3.59-3.95120.08215663.8031100
3.95-4.5211.60.07515644.3721100
4.52-5.711.70.07215944.7581100
5.7-4011.10.06716575.8871100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1731 / WRfactor Rwork: 0.1394 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.9125 / SU B: 6.302 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1711 / SU Rfree: 0.1437 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 1552 5 %RANDOM
Rwork0.141 ---
obs0.1429 30862 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.25 Å2 / Biso mean: 35.1945 Å2 / Biso min: 20.27 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 0 348 4115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193844
X-RAY DIFFRACTIONr_bond_other_d0.0060.023742
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.975212
X-RAY DIFFRACTIONr_angle_other_deg1.10138559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1295504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83423.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73615584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.9631530
X-RAY DIFFRACTIONr_chiral_restr0.1140.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214421
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02853
Refine LS restraints NCS

Ens-ID: 1 / Number: 14449 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 96 -
Rwork0.156 2171 -
all-2267 -
obs--100 %
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)
10.5364-0.0625-0.10420.5284-0.08440.5158-0.01480.028-0.1441-0.0701-0.0029-0.05390.09030.04510.01780.07950.0210.02180.0476-0.01210.096334.9948.35921.153
20.45050.1891-0.0240.5919-0.090.4076-0.0070.0055-0.0596-0.02720.0095-0.1551-0.00140.0605-0.00250.01930.00890.00850.03920.00270.08957.24432.09538.748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 257
2X-RAY DIFFRACTION2B4 - 257

+
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