[English] 日本語
Yorodumi
- PDB-6mfh: Mutated Uronate Dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mfh
TitleMutated Uronate Dehydrogenase
ComponentsMutated Uronate Dehydrogenase
KeywordsOXIDOREDUCTASE / mutated / uronate dehydrogenase
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / PHOSPHATE ION / NAD-dependent epimerase/dehydratase
Function and homology information
Biological speciesChromohalobacter salexigens DSM 3043 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSankaran, B. / Pereira, J.H. / Chan, V. / Zwart, P.H. / Wagschal, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P30GM124169-01 United States
CitationJournal: Process Biochem / Year: 2020
Title: Chromohalobacter salixigens uronate dehydrogenase: Directed evolution for improved thermal stability and mutant CsUDH-inc X-ray crystal structure
Authors: Wagschal, K. / Chan, V. / Pereira, J.H. / Zwart, P.H. / Sankaran, B.
History
DepositionSep 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mutated Uronate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1166
Polymers30,4631
Non-polymers6535
Water4,414245
1
A: Mutated Uronate Dehydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)186,69636
Polymers182,7806
Non-polymers3,91630
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_555-y+3/4,-x+3/4,-z+3/41
crystal symmetry operation19_555-x+3/4,-z+3/4,-y+3/41
crystal symmetry operation24_555-z+3/4,-y+3/4,-x+3/41
Buried area25750 Å2
ΔGint-205 kcal/mol
Surface area61570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.098, 197.098, 197.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

21A-451-

HOH

31A-453-

HOH

41A-492-

HOH

51A-530-

HOH

61A-641-

HOH

-
Components

#1: Protein Mutated Uronate Dehydrogenase / NAD-dependent epimerase/dehydratase


Mass: 30463.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The final construct was based on a DNA shuffle using Chromohalobacter salexigens and Polaromonas naphthalenivorans
Source: (gene. exp.) Chromohalobacter salexigens DSM 3043 (bacteria)
Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: CSAL / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QUN7*PLUS, Oxidoreductases
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 5.26 Å3/Da / Density % sol: 76.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 30% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2→69.7 Å / Num. obs: 41593 / % possible obs: 100 % / Redundancy: 47 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.3 / Rpim(I) all: 0.044 / Rrim(I) all: 0.3 / Net I/σ(I): 18
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 5.2 / Num. unique obs: 4107 / CC1/2: 0.715 / Rpim(I) all: 0.76 / Rrim(I) all: 5.26 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
xia20.4.0.338data reduction
xia2data scaling
PHASER1.13phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AY3

3ay3


Resolution: 2.04→69.685 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.2319 1635 4.81 %
Rwork0.206 --
obs0.2073 34023 81.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.04→69.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 34 245 2423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042249
X-RAY DIFFRACTIONf_angle_d0.5793059
X-RAY DIFFRACTIONf_dihedral_angle_d9.8811316
X-RAY DIFFRACTIONf_chiral_restr0.044332
X-RAY DIFFRACTIONf_plane_restr0.003398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0401-2.10010.3251380.3312581X-RAY DIFFRACTION80
2.1001-2.16790.32351600.31643184X-RAY DIFFRACTION98
2.1679-2.24540.38441270.312693X-RAY DIFFRACTION82
2.2454-2.33530.25761050.28842172X-RAY DIFFRACTION67
2.3353-2.44160.37071120.27492164X-RAY DIFFRACTION67
2.4416-2.57030.29051150.24962327X-RAY DIFFRACTION71
2.5703-2.73140.25141180.2412408X-RAY DIFFRACTION73
2.7314-2.94230.2561330.21112593X-RAY DIFFRACTION79
2.9423-3.23840.19591380.19422683X-RAY DIFFRACTION82
3.2384-3.70690.21621480.16832956X-RAY DIFFRACTION89
3.7069-4.67020.17031650.13983170X-RAY DIFFRACTION94
4.6702-69.72530.18831760.17413457X-RAY DIFFRACTION98
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)
16.9831-0.79020.574.59040.19153.6882-0.0992-0.44920.55390.36440.01780.1137-0.33880.03760.07190.29040.02060.03190.1621-0.02170.215568.8244115.295382.9413
25.02062.132-0.03095.00712.37033.6543-0.18010.23070.6798-0.12-0.02580.2357-0.4783-0.23430.20240.26180.04350.03160.18820.10130.320560.1137114.645874.0687
34.695.11320.04076.0296-0.65282.65260.08090.09630.40240.1940.09480.3343-0.0977-0.088-0.15340.21210.06390.06330.214-0.01810.279151.7793101.383383.6958
46.96144.626-2.22474.5381-0.16861.94430.02410.04360.4799-0.15090.01160.40090.01670.0654-0.090.21910.05910.00940.1810.03060.26258.3591106.322169.0133
50.9003-0.47120.1425.3352-1.62710.45740.05050.0013-0.0412-0.0881-0.10770.10130.02390.03760.05940.17750.02740.03080.19040.00240.133565.110689.910381.1572
61.74221.2087-3.11070.8421-1.98557.57060.1338-0.1033-0.017-0.0516-0.00250.12090.07060.3141-0.04150.20570.03860.02330.22520.0350.244360.23995.711873.3769
70.9346-0.48590.671.5379-1.23292.15870.0247-0.0430.04680.1569-0.0409-0.033-0.1743-0.01160.01670.21630.02230.0320.19610.01740.212773.875496.284583.769
83.08811.9272-0.05685.92930.10824.40160.4319-0.69760.23321.1263-0.2183-0.1477-0.2257-0.1773-0.09780.41040.0670.05870.28450.00630.1570.443988.0171104.8274
92.72042.01640.57151.6851-0.1812.6864-0.0744-0.35960.7840.25210.1820.3769-0.2587-0.57560.00740.29070.05920.11390.34370.0360.318649.149492.009393.4456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 100 )
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 133 )
6X-RAY DIFFRACTION6chain 'A' and (resid 134 through 151 )
7X-RAY DIFFRACTION7chain 'A' and (resid 152 through 229 )
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 247 )
9X-RAY DIFFRACTION9chain 'A' and (resid 248 through 277 )

+
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