[English] 日本語
Yorodumi
- PDB-4h15: Crystal Structure of a short chain alcohol dehydrogenase-related ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h15
TitleCrystal Structure of a short chain alcohol dehydrogenase-related dehydrogenase (target ID NYSGRC-011812) from Sinorhizobium meliloti 1021 in space group P21
ComponentsShort chain alcohol dehydrogenase-related dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / NYSGRC / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


monocarboxylic acid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / lipid metabolic process / oxidoreductase activity / metal ion binding
Similarity search - Function
: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Short chain alcohol dehydrogenase-related dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsGhosh, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of a short chain alcohol dehydrogenase-related dehydrogenase (target ID NYSGRC-011812) from Sinorhizobium meliloti 1021 in space group P21
Authors: Ghosh, A. / Bhoshle, R. / Toro, R. / Gizzi, A. / Hillerich, B. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 alcohol dehydrogenase-related dehydrogenase
B: Short chain alcohol dehydrogenase-related dehydrogenase
C: Short chain alcohol dehydrogenase-related dehydrogenase
D: Short chain alcohol dehydrogenase-related dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,22367
Polymers109,9464
Non-polymers3,27763
Water16,952941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24830 Å2
ΔGint-781 kcal/mol
Surface area35590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.304, 119.143, 67.156
Angle α, β, γ (deg.)90.000, 105.830, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThere is 1 biological unit (a tetramer) in the asymmetric unit (chain A, B, C, D)

-
Components

#1: Protein
Short chain alcohol dehydrogenase-related dehydrogenase


Mass: 27486.529 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0888, SMa1629 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRIL
References: UniProt: Q92YJ2, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 941 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Calcium Chloride 0.1 M Bis-Tris:HCl, 45% (v/v) MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2012
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 170863 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.03 / Χ2: 1.106 / Net I/σ(I): 27.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.482.10.148160491.307193.8
1.48-1.52.10.13161781.25194.2
1.5-1.532.10.115163301.221194.7
1.53-1.562.10.098164701.141195.1
1.56-1.62.10.089164691.094195.6
1.6-1.632.10.08165171.278195.8
1.63-1.672.10.071166441.203196.4
1.67-1.722.10.063165731.123196.8
1.72-1.772.10.057167441.07197.2
1.77-1.832.10.05167810.977197.6
1.83-1.892.10.043168881.012198
1.89-1.972.10.038169471.006198.3
1.97-2.062.10.033169821.046198.7
2.06-2.172.10.031170881.098198.9
2.17-2.32.10.032170301.044198.9
2.3-2.482.10.034170801.048199.2
2.48-2.7320.031170391.001199.1
2.73-3.1220.023168481.004197.8
3.12-3.941.90.018161721.115193.9
3.94-5020.017145071.068184.1

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→27.787 Å / Occupancy max: 1 / Occupancy min: 0.04 / FOM work R set: 0.9082 / SU ML: 0.11 / σ(F): 1.35 / Phase error: 15.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1672 8550 5 %RANDOM
Rwork0.1496 ---
obs0.1505 170860 98.05 %-
all-170863 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.05 Å2 / Biso mean: 16.9524 Å2 / Biso min: 3.37 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7632 0 147 941 8720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078174
X-RAY DIFFRACTIONf_angle_d1.16111174
X-RAY DIFFRACTIONf_chiral_restr0.0741348
X-RAY DIFFRACTIONf_plane_restr0.0061441
X-RAY DIFFRACTIONf_dihedral_angle_d12.7883091
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 (%)
1.4499-1.46640.19842540.17174938519290
1.4664-1.48360.20692780.1725526580499
1.4836-1.50170.19882680.167854545722100
1.5017-1.52070.19442720.172355595831100
1.5207-1.54070.16772920.161254295721100
1.5407-1.56180.18472890.152455645853100
1.5618-1.58410.16632840.147654065690100
1.5841-1.60780.17022920.147955105802100
1.6078-1.63290.16663050.145655445849100
1.6329-1.65970.18542790.142954515730100
1.6597-1.68830.14382880.144654825770100
1.6883-1.7190.1743030.150655135816100
1.719-1.7520.17392710.151854925763100
1.752-1.78780.15733090.155554655774100
1.7878-1.82670.16852830.144355075790100
1.8267-1.86920.17183010.145355065807100
1.8692-1.91590.16322870.147355405827100
1.9159-1.96770.16042940.150554405734100
1.9677-2.02560.17953070.147154935800100
2.0256-2.09090.1593000.140354855785100
2.0909-2.16560.17162830.144355435826100
2.1656-2.25230.15333210.13675414573599
2.2523-2.35470.15852810.13855500578199
2.3547-2.47880.16162860.14245500578699
2.4788-2.6340.16722920.14925453574599
2.634-2.83720.17182660.14155507577399
2.8372-3.12240.16462650.14455392565797
3.1224-3.57340.15392840.14245177546194
3.5734-4.4990.14852810.14474947522889
4.499-27.7920.20362350.19474573480881
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)
11.81280.80160.41660.5556-0.1571.59230.0622-0.1774-0.16860.2797-0.0141-0.35910.15940.063-0.02710.18170.0189-0.07460.13550.04350.1488-15.50728.14681.2146
20.3541-0.5102-0.03991.08930.69611.07520.0928-0.2641-0.30760.5818-0.04790.10890.35-0.0617-0.0470.2863-0.0223-0.04340.17670.06470.1713-25.9055-1.22852.9006
30.5046-0.0937-0.23820.61910.12260.82860.0211-0.0857-0.06540.1325-0.0029-0.02530.08310.011-0.00480.0686-0.0041-0.01550.05750.01510.0625-28.48295.5564-13.695
41.4692-0.1770.00510.9603-0.30151.3856-0.00940.1247-0.1489-0.0326-0.0733-0.17650.12850.27390.05050.06370.0106-0.01040.08740.0010.1109-14.609914.7024-19.0385
51.15080.7441.11452.23721.92222.47770.09910.0363-0.0162-0.054-0.11560.2050.1694-0.17640.00050.15580.0133-0.04750.1080.0240.0916-51.523524.847-49.1496
61.37940.0660.78572.53711.16032.1411-0.25050.46740.3642-0.77550.2557-0.2136-0.70420.17980.07450.3398-0.0403-0.04450.16990.05610.1891-46.990640.8411-50.3225
73.19190.5158-0.30752.2032-0.55811.0144-0.00880.12450.4851-0.0964-0.07290.4177-0.5066-0.1910.04360.21980.0486-0.04980.13110.00810.1581-52.906742.8058-41.4998
80.8120.17140.09780.6905-0.01190.3697-0.02440.02990.0669-0.0640.00340.0574-0.0605-0.03080.01560.05810.00620.00160.04570.00010.0435-39.001835.0021-33.0002
95.50291.4971-3.09641.8653-0.66733.51560.11580.76320.6503-0.8004-0.231-0.4120.08260.31510.13110.314-0.01070.10750.38530.10320.3389-19.800627.3192-49.5486
101.7096-0.32390.05220.7444-0.11011.05490.06240.1071-0.033-0.1189-0.01740.0267-0.0011-0.0057-0.03330.0517-0.0042-0.00340.0189-0.0040.0276-39.964620.4113-40.0755
112.2376-0.7170.80582.3409-0.91582.8709-0.0260.2260.1156-0.4419-0.03740.2741-0.1159-0.03510.04370.1746-0.0349-0.05820.0979-0.02120.1686-51.6996.1717-44.954
122.17810.17490.84111.18480.04410.35180.0974-0.1599-0.3879-0.02420.27560.28280.3477-0.4492-0.28410.1724-0.0604-0.03990.15230.02920.202-52.4561-7.6818-37.3734
132.1772-0.2335-0.38394.34440.13454.2217-0.02550.1329-0.5052-0.4196-0.0805-0.27680.58410.17440.04420.13800.02820.1041-0.040.1982-41.3214-8.6833-40.0276
140.3509-0.15240.52390.4238-0.9834.42170.0957-0.0932-0.0465-0.0037-0.01480.07470.3009-0.1973-0.10090.1133-0.03510.00910.08250.020.098-42.7545-1.8062-16.065
153.82680.5053-2.62422.6048-0.05436.2455-0.01380.0757-0.2811-0.1449-0.08-0.1220.4142-0.13470.03980.07040.0017-0.00720.0456-0.01980.0957-34.4233-3.6072-36.7077
160.58760.03760.0660.89590.07020.74990.0219-0.015-0.0615-0.0163-0.00130.03080.0835-0.0439-0.01090.032-0.0047-0.00870.03280.00380.0431-38.94137.9284-28.3468
176.3376-1.0937-3.54344.72111.1247.3564-0.0242-0.6695-0.68470.766-0.19170.57240.9827-0.40690.1970.306-0.08290.01340.21120.06180.3334-61.40545.0892-15.8052
181.01160.09880.17791.04530.34520.81920.0086-0.1201-0.02770.0393-0.06260.1870.0311-0.21120.02150.0329-0.0026-0.00110.07540.00530.0748-51.05915.4081-27.8232
191.3440.06180.72241.21980.16792.2594-0.0078-0.09290.09720.2470.0139-0.1823-0.12560.094-0.00690.1686-0.0324-0.01250.0994-0.02580.1021-18.36343.3192-5.8599
200.70540.04060.18740.80960.01940.5144-0.0229-0.07420.07760.0496-0.0061-0.029-0.07440.00720.020.06070.00040.0030.0497-0.00640.0411-29.295737.5211-19.1636
210.9812-0.95690.28761.77240.8481.7258-0.1973-1.13630.64590.8664-0.17380.9683-0.115-0.7270.33990.36620.06590.0550.5217-0.19240.552-48.644736.4117-1.7276
221.77140.4957-0.33160.89680.2651.10460.0499-0.1401-0.01890.1617-0.045-0.0277-0.0115-0.0087-0.0010.08080.0003-0.00810.04580.01530.0266-28.664326.1674-7.7745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 59 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 82 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 186 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 187 through 259 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 31 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 59 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 82 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 83 through 186 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 187 through 215 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 216 through 259 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid -1 through 31 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 32 through 59 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 60 through 82 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 83 through 110 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 111 through 127 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 128 through 186 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 187 through 200 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 201 through 259 )C0
19X-RAY DIFFRACTION19chain 'D' and (resid -1 through 82 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 83 through 186 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 187 through 214 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 215 through 259 )D0

+
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