[English] 日本語
Yorodumi
- PDB-4idg: Crystal structure of a short-chain dehydrogenase/reductase superf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4idg
TitleCrystal structure of a short-chain dehydrogenase/reductase superfamily protein from agrobacterium tumefaciens (TARGET EFI-506441) with bound NAD, monoclinic form 2
ComponentsSHORT-CHAIN DEHYDROGENASE/REDUCTASE
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


UDP-galactose 4-epimerase; domain 1 - #60 / : / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVetting, M.W. / Groninger-Poe, F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a short-chain dehydrogenase/reductase superfamily protein from agrobacterium tumefaciens (TARGET EFI-506441) with bound NAD, monoclinic form 2
Authors: Vetting, M.W. / Groninger-Poe, F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionDec 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
B: SHORT-CHAIN DEHYDROGENASE/REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,84911
Polymers76,1682
Non-polymers1,6819
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-9 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.388, 57.703, 95.418
Angle α, β, γ (deg.)90.000, 108.680, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein SHORT-CHAIN DEHYDROGENASE/REDUCTASE


Mass: 38083.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (bacteria) / Strain: str. C58 / Gene: galE, Atu5463 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CL58
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 6.5
Details: Protein (10mM Tris pH 7.9, 5 mM NAD, 5 mM UDP-GAL; Reservoir (0.1 M Bis-Tris:HCl pH 6.5 20% (w/v) PEG MME 5000); Cryoprotection (Reservoir + 20% ethylene glycol, 5 mM NAD, 5 mM UDP-GAL), ...Details: Protein (10mM Tris pH 7.9, 5 mM NAD, 5 mM UDP-GAL; Reservoir (0.1 M Bis-Tris:HCl pH 6.5 20% (w/v) PEG MME 5000); Cryoprotection (Reservoir + 20% ethylene glycol, 5 mM NAD, 5 mM UDP-GAL), sitting drop vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 8, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→90.391 Å / Num. all: 61811 / Num. obs: 61811 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.058 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-23.20.5821.42875089290.58297.7
2-2.123.40.2872.82922485640.28798.9
2.12-2.273.60.19642898281100.19699.4
2.27-2.453.70.1415.62763375360.14199.7
2.45-2.693.70.1017.62580569830.10199.5
2.69-33.70.0710.62314362990.0798.9
3-3.473.60.04813.51963254530.04897.4
3.47-4.253.50.03716.71593944960.03794.3
4.25-6.013.60.028221304536030.02896.9
6.01-90.3913.40.02426.2627818380.02488

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ID9

4id9


Resolution: 1.9→35.746 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.7894 / SU ML: 0.19 / σ(F): 0 / σ(I): 0 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 3127 5.07 %RANDOM
Rwork0.1767 ---
all0.1787 ---
obs0.1787 61676 97.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112 Å2 / Biso mean: 26.2121 Å2 / Biso min: 1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5072 0 107 460 5639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065334
X-RAY DIFFRACTIONf_angle_d1.0487240
X-RAY DIFFRACTIONf_chiral_restr0.071788
X-RAY DIFFRACTIONf_plane_restr0.005968
X-RAY DIFFRACTIONf_dihedral_angle_d14.2961978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92970.29931400.28222659279997
1.9297-1.96140.30531520.26862577272997
1.9614-1.99520.32631460.25172685283197
1.9952-2.03150.29821450.23582621276698
2.0315-2.07050.28621620.21422647280998
2.0705-2.11280.23761430.20782675281899
2.1128-2.15870.24771490.19542661281099
2.1587-2.20890.22751560.18072698285499
2.2089-2.26420.2221350.17182683281899
2.2642-2.32540.2211470.17882691283899
2.3254-2.39380.22171240.17922720284499
2.3938-2.4710.22741350.17782704283999
2.471-2.55930.2561310.16942690282199
2.5593-2.66180.23081520.1812715286799
2.6618-2.78280.22191310.17722711284299
2.7828-2.92950.23581300.18322689281998
2.9295-3.11290.21661490.19152662281198
3.1129-3.35310.2021400.16312651279197
3.3531-3.69030.17741270.1652609273695
3.6903-4.22350.18911340.15252587272194
4.2235-5.31840.16121620.14272655281796
5.3184-35.75210.22861370.17982559269690
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)
11.0988-0.09130.27241.02460.15321.4937-0.0731-0.06720.380.027-0.05180.3462-0.2447-0.19720.05450.14740.0274-0.02760.1005-0.03520.2245.105315.140137.9049
20.5483-0.02190.18761.0187-0.11140.94030.00240.00450.0016-0.1357-0.01240.08750.04060.02130.01410.065-0.0026-0.0270.0677-0.00270.079310.6749-0.721931.2249
30.44440.0613-0.09590.5416-0.09220.81050.1229-0.13430.010.5011-0.11110.07620.0995-0.14970.03330.2346-0.07040.06130.1707-0.03470.09034.5198-4.738452.4888
40.5877-0.08290.20490.8790.32591.04580.0161-0.04250.0597-0.1954-0.00770.0789-0.02370.0263-0.00730.0699-0.0266-0.04750.06370.00470.08785.6626-8.959111.8996
50.62750.027-0.06290.30210.17170.66340.26740.1241-0.1432-0.25390.2251-0.2254-0.360.40080.29620.3587-0.10590.26130.221-0.13340.056922.2517-6.6249-1.3274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 71 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 149 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 327 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 149 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 150 through 327 )B0

+
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