[English] 日本語
Yorodumi
- PDB-3uxy: The crystal structure of short chain dehydrogenase from Rhodobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uxy
TitleThe crystal structure of short chain dehydrogenase from Rhodobacter sphaeroides
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.097 Å
AuthorsZhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: The crystal structure of short chain dehydrogenase from Rhodobacter sphaeroides
Authors: Zhang, Z. / Almo, S.C. / Swaminathan, S.
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7055
Polymers110,0424
Non-polymers6631
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-95 kcal/mol
Surface area31780 Å2
MethodPISA
2
A: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6843
Polymers55,0212
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-33 kcal/mol
Surface area18330 Å2
MethodPISA
3
A: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)55,0212
Polymers55,0212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-16 kcal/mol
Surface area19110 Å2
MethodPISA
4
B: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)55,0212
Polymers55,0212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-27 kcal/mol
Surface area18750 Å2
MethodPISA
5
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6843
Polymers55,0212
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-23 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.526, 87.999, 93.463
Angle α, β, γ (deg.)90.00, 111.68, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Short-chain dehydrogenase/reductase SDR


Mass: 27510.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RHOS4_38900, RSP_4006 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q3IVH6
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M sodium chloride, 0.1 M tris pH 5.5, 25% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 58020 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 12.1 / Num. unique all: 2704 / % possible all: 87.9

-
Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.097→43.427 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 20.22 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 2947 5.09 %RANDOM
Rwork0.1699 ---
obs0.1721 57921 98.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.965 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4287 Å20 Å2-3.4752 Å2
2---0.3747 Å2-0 Å2
3---1.7295 Å2
Refinement stepCycle: LAST / Resolution: 2.097→43.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6809 0 44 578 7431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086957
X-RAY DIFFRACTIONf_angle_d1.1739482
X-RAY DIFFRACTIONf_dihedral_angle_d16.2632473
X-RAY DIFFRACTIONf_chiral_restr0.0751115
X-RAY DIFFRACTIONf_plane_restr0.0051256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0969-2.13130.21941130.15462336X-RAY DIFFRACTION89
2.1313-2.16810.22621280.15562561X-RAY DIFFRACTION97
2.1681-2.20750.24851230.14752601X-RAY DIFFRACTION98
2.2075-2.24990.19691400.15722597X-RAY DIFFRACTION99
2.2499-2.29590.20221410.15452636X-RAY DIFFRACTION99
2.2959-2.34580.2261180.1612631X-RAY DIFFRACTION99
2.3458-2.40030.18911530.15112579X-RAY DIFFRACTION99
2.4003-2.46040.20271390.15962642X-RAY DIFFRACTION99
2.4604-2.52690.19581460.1662619X-RAY DIFFRACTION99
2.5269-2.60120.22341180.17822628X-RAY DIFFRACTION99
2.6012-2.68520.22991450.18182596X-RAY DIFFRACTION98
2.6852-2.78110.26561720.18122591X-RAY DIFFRACTION99
2.7811-2.89250.23931480.18462655X-RAY DIFFRACTION100
2.8925-3.02410.22471440.18482627X-RAY DIFFRACTION100
3.0241-3.18350.25011400.18222647X-RAY DIFFRACTION100
3.1835-3.38280.20681430.17242647X-RAY DIFFRACTION100
3.3828-3.64390.20371460.1672655X-RAY DIFFRACTION100
3.6439-4.01040.18311320.15842671X-RAY DIFFRACTION100
4.0104-4.59010.18991500.15222675X-RAY DIFFRACTION100
4.5901-5.7810.17941600.16342666X-RAY DIFFRACTION100
5.781-43.43660.19741480.18812714X-RAY DIFFRACTION99

+
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