[English] 日本語
Yorodumi
- PDB-4e4u: Crystal structure of a putative Mandelate racemase/Muconate lacto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e4u
TitleCrystal structure of a putative Mandelate racemase/Muconate lactonizing enzyme (Target PSI-200780) from Burkholderia SAR-1
ComponentsMandalate racemase/muconate lactonizing enzyme
KeywordsISOMERASE / Racemase / Mandelate racemase / aldolase / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homologyEnolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKumar, P.R. / Bonanno, J. / Chowdhury, S. / Foti, R. / Gizzi, A. / Hammonds, J. / Hillerich, B. / Matikainen, B. / Seidel, R. / Toro, R. ...Kumar, P.R. / Bonanno, J. / Chowdhury, S. / Foti, R. / Gizzi, A. / Hammonds, J. / Hillerich, B. / Matikainen, B. / Seidel, R. / Toro, R. / Zencheck, W. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a putative MR/ML enzyme from Burkholderia SAR-1
Authors: Kumar, P.R. / Bonanno, J. / Chowdhury, S. / Foti, R. / Gizzi, A. / Hammonds, J. / Hillerich, B. / Matikainen, B. / Seidel, R. / Toro, R. / Zencheck, W. / Almo, S.C.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Mandalate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8022
Polymers45,6481
Non-polymers1541
Water7,638424
1
A: Mandalate racemase/muconate lactonizing enzyme
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)366,41916
Polymers365,1858
Non-polymers1,2348
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_554-x,y,-z-11
crystal symmetry operation6_554x,-y,-z-11
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation8_554-y,-x,-z-11
Buried area48150 Å2
ΔGint-208 kcal/mol
Surface area84430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.835, 118.835, 120.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-774-

HOH

31A-776-

HOH

41A-827-

HOH

51A-1011-

HOH

DetailsThe biological assembly is an octamer generated by crystallographic symmetry operations

-
Components

#1: Protein Mandalate racemase/muconate lactonizing enzyme


Mass: 45648.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: from Sargasso sea / Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (2.5M NaCl, Sodium Acetate 4.5, 0.2M Li2SO4- Wizard II #38); Cryoprotection (LI2SO4), Sitting Drop Vapor Diffusion, ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (2.5M NaCl, Sodium Acetate 4.5, 0.2M Li2SO4- Wizard II #38); Cryoprotection (LI2SO4), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionHighest resolution: 1.35 Å / Num. obs: 181393 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.261 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.05
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.35-1.391.91166711326798.9
1.39-1.422.5414225813129100
1.42-1.463.314428212755100
1.46-1.514.5414475812370100
1.51-1.565.6614471411925100
1.56-1.617.2414636011644100
1.61-1.679.1714579311201100
1.67-1.7411.3714472410738100
1.74-1.8213.9814444010341100
1.82-1.9117.611422659872100
1.91-2.0121.96138249938899.9
2.01-2.1325.911305978831100
2.13-2.2829.141233528364100
2.28-2.4631.421154137795100
2.46-2.733.691049787132100
2.7-3.0235.92936786443100
3.02-3.4938.86819205705100
3.49-4.2742.22719094806100
4.27-6.0442.755557372999.9
6.0440.9927179195895.7

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
XDSdata reduction
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→37.641 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.934 / SU ML: 0.16 / σ(F): 1.34 / Phase error: 12.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1461 4719 5.02 %
Rwork0.1331 --
obs0.1338 94064 99.83 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.327 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 59.07 Å2 / Biso mean: 17.8719 Å2 / Biso min: 5.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.1269 Å20 Å2-0 Å2
2--0.1269 Å20 Å2
3----0.2538 Å2
Refinement stepCycle: LAST / Resolution: 1.35→37.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 8 424 3571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053315
X-RAY DIFFRACTIONf_angle_d1.1244519
X-RAY DIFFRACTIONf_chiral_restr0.071495
X-RAY DIFFRACTIONf_plane_restr0.005591
X-RAY DIFFRACTIONf_dihedral_angle_d13.0321231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.36530.27731370.24342900303798
1.3653-1.38140.23291770.21432926310399
1.3814-1.39830.19261420.192329633105100
1.3983-1.4160.20011630.178329163079100
1.416-1.43460.18391530.165329673120100
1.4346-1.45420.18121530.150729443097100
1.4542-1.4750.16741610.142529543115100
1.475-1.4970.16031390.135429663105100
1.497-1.52040.17241620.127129543116100
1.5204-1.54540.14231510.118629723123100
1.5454-1.5720.14271590.11529483107100
1.572-1.60060.14461570.108229433100100
1.6006-1.63140.15351760.110829493125100
1.6314-1.66470.14391490.10729743123100
1.6647-1.70090.13511660.104829583124100
1.7009-1.74040.14431480.102129633111100
1.7404-1.7840.14241530.108629983151100
1.784-1.83220.14561270.107829783105100
1.8322-1.88610.13831740.109629763150100
1.8861-1.9470.15211680.114529633131100
1.947-2.01660.13471630.117629633126100
2.0166-2.09730.15531680.118629513119100
2.0973-2.19270.14851560.120930173173100
2.1927-2.30830.13321500.123429823132100
2.3083-2.45290.1441500.126930173167100
2.4529-2.64230.13121500.134430313181100
2.6423-2.90810.15881490.145230273176100
2.9081-3.32870.151670.148330303197100
3.3287-4.19290.1261760.126430613237100
4.1929-37.65550.13821750.15853154332998

+
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