[English] 日本語
Yorodumi
- PDB-4knp: Crystal Structure Of a Putative enoyl-coA hydratase (PSI-NYSGRC-0... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4knp
TitleCrystal Structure Of a Putative enoyl-coA hydratase (PSI-NYSGRC-019597) from Mycobacterium avium paratuberculosis K-10
Componentsenoyl-CoA hydratase
KeywordsLYASE / Enoyl-coA / hydratase / Protein structure initiative / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


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 ...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
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 1.898 Å
AuthorsKumar, P.R. / Ahmed, M. / Attonito, J. / Bhosle, R. / Chamala, S. / Chowdhury, S. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Love, J.D. ...Kumar, P.R. / Ahmed, M. / Attonito, J. / Bhosle, R. / Chamala, S. / Chowdhury, S. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Love, J.D. / Seidel, R. / Stead, M. / Toro, R. / Wasserman, S.R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a Putative enoyl-coA hydratase from Mycobacterium avium paratuberculosis K-10
Authors: Kumar, P.R. / Hillerich, B. / Love, J. / Seidel, R. / Almo, S.C.
History
DepositionMay 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)30,1901
Polymers30,1901
Non-polymers00
Water1,33374
1
A: enoyl-CoA hydratase

A: enoyl-CoA hydratase

A: enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)90,5703
Polymers90,5703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7080 Å2
ΔGint-33 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.971, 80.971, 91.364
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein enoyl-CoA hydratase


Mass: 30189.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: K-10 / Gene: echA7, MAP_0909c / Plasmid: pSGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q742C8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.91 Å3/Da / Density % sol: 35.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (0.2M Calcium Acetate, 40% PEG 300, 0.1M Sodium Cacodylate, pH(6.5) - MCSG1 #46); Cryoprotection (Xylitol), Vapor ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (0.2M Calcium Acetate, 40% PEG 300, 0.1M Sodium Cacodylate, pH(6.5) - MCSG1 #46); Cryoprotection (Xylitol), Vapor Diffusion, Sitting Drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 28, 2013 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.36
ReflectionResolution: 1.9→50 Å / Num. all: 17671 / Num. obs: 17650 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.083 / Χ2: 1.411 / Net I/σ(I): 27.93
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.936.40.9139031.0321100
1.93-1.976.40.7938780.9811100
1.97-2.016.40.6738710.9981100
2.01-2.056.40.5698801.0321100
2.05-2.096.40.478861.0751100
2.09-2.146.40.3739121.0821100
2.14-2.196.40.3338561.0851100
2.19-2.256.40.2988811.1221100
2.25-2.326.50.248971.1261100
2.32-2.396.50.1888721.1221100
2.39-2.486.50.158801.0831100
2.48-2.586.50.1358711.1331100
2.58-2.76.50.1258891.171100
2.7-2.846.50.1018951.3281100
2.84-3.026.50.0948621.6641100
3.02-3.256.30.088922.2311100
3.25-3.586.10.0668812.5431100
3.58-4.096.30.059022.4781100
4.09-5.166.50.0358791.7151100
5.16-506.30.048632.347197.8

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
DENZOdata reduction
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: 3OC7

3oc7


Resolution: 1.898→25.455 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8277 / σ(F): 1.96 / Phase error: 25.29 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1654 896 5.08 %RANDOM
Rwork0.1329 ---
obs0.1354 17650 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.42 Å2 / Biso mean: 35.199 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: LAST / Resolution: 1.898→25.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 0 74 1915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081899
X-RAY DIFFRACTIONf_angle_d1.0832578
X-RAY DIFFRACTIONf_chiral_restr0.071301
X-RAY DIFFRACTIONf_plane_restr0.005344
X-RAY DIFFRACTIONf_dihedral_angle_d13.579694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8983-2.01710.24621730.22442772294594
2.0171-2.17270.20581500.1882777292795
2.1727-2.39090.18231450.162811295695
2.3909-2.73590.17361500.14352785293595
2.7359-3.44340.15181510.12352784293595
3.4434-18.54330.14111270.10652807293495
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)
16.85915.25981.30688.98960.76832.777-0.01780.0550.31740.01240.03260.4887-0.4245-0.2959-0.01030.2690.13620.02930.23120.01830.246619.215245.841130.2408
21.4767-0.65461.12270.5442-0.03072.0047-0.0128-0.11530.4552-0.0826-0.07550.2155-0.1312-0.03680.11580.26970.06540.0480.2603-0.00340.259724.127943.868528.9815
32.66640.08810.06380.4563-0.04740.96540.0897-0.02180.2891-0.0676-0.01550.0136-0.2025-0.0143-0.06290.20910.03030.04140.14870.02020.223135.526740.188431.3275
42.68250.99780.23741.62250.16811.41120.05050.00260.1209-0.07460.0125-0.0043-0.07470.01-0.05540.19250.06730.0180.1310.00960.237233.832536.351531.1387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 60 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 94 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 182 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 262 )A0

+
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://pdbjlvh1.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