[English] 日本語
Yorodumi
- PDB-6xex: Structure of Serratia marcescens 2,3-butanediol dehydrogenase mut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xex
TitleStructure of Serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A/V139Q
Components2,3-butanediol dehydrogenase
KeywordsOXIDOREDUCTASE / BDH
Function / homologyOxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Meso-2,3-butanediol dehydrogenase
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Biotechnol Biofuels / Year: 2020
Title: Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression.
Authors: Subramanian, V. / Lunin, V.V. / Farmer, S.J. / Alahuhta, M. / Moore, K.T. / Ho, A. / Chaudhari, Y.B. / Zhang, M. / Himmel, M.E. / Decker, S.R.
History
DepositionJun 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: 2,3-butanediol dehydrogenase
B: 2,3-butanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,84310
Polymers55,8232
Non-polymers1,0208
Water9,764542
1
A: 2,3-butanediol dehydrogenase
B: 2,3-butanediol dehydrogenase
hetero molecules

A: 2,3-butanediol dehydrogenase
B: 2,3-butanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,68620
Polymers111,6474
Non-polymers2,03916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area21340 Å2
ΔGint-148 kcal/mol
Surface area31520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.800, 108.800, 83.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein 2,3-butanediol dehydrogenase / 3-oxoacyl-ACP reductase / SDR family oxidoreductase


Mass: 27911.709 Da / Num. of mol.: 2 / Mutation: Q247A/V139Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: budC, A8A12_06140, FG174_10665 / Production host: Zymomonas mobilis (bacteria) / References: UniProt: H9XP47, Oxidoreductases
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate, pH 6-7, 6-15% w/v PEG3350 / PH range: 6-7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Dec 28, 2017 / Details: HELIOS MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→42.025 Å / Num. obs: 46796 / % possible obs: 100 % / Redundancy: 16.99 % / Rsym value: 0.0925 / Net I/σ(I): 21.68
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 1.91 / Num. unique obs: 6911 / Rsym value: 0.7928

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NI5

4ni5


Resolution: 1.8→42.025 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.871 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.121
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2095 2318 4.97 %
Rwork0.1603 44318 -
all0.163 --
obs-46636 99.782 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.962 Å2
Baniso -1Baniso -2Baniso -3
1-0.139 Å2-0 Å2-0 Å2
2--0.139 Å2-0 Å2
3----0.279 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 66 542 4289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133897
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173668
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.6255293
X-RAY DIFFRACTIONr_angle_other_deg1.4851.5828460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6135521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71622.186183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21615612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8241526
X-RAY DIFFRACTIONr_chiral_restr0.0810.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024525
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02808
X-RAY DIFFRACTIONr_nbd_refined0.220.2823
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.23486
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21932
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21635
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2402
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1390.25
X-RAY DIFFRACTIONr_metal_ion_refined0.1890.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.231
X-RAY DIFFRACTIONr_nbd_other0.1960.2128
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.252
X-RAY DIFFRACTIONr_mcbond_it1.9282.1962063
X-RAY DIFFRACTIONr_mcbond_other1.9272.1952062
X-RAY DIFFRACTIONr_mcangle_it2.6413.2892591
X-RAY DIFFRACTIONr_mcangle_other2.643.292592
X-RAY DIFFRACTIONr_scbond_it2.6832.5561834
X-RAY DIFFRACTIONr_scbond_other2.6822.5571835
X-RAY DIFFRACTIONr_scangle_it4.0473.6912702
X-RAY DIFFRACTIONr_scangle_other4.0463.6922703
X-RAY DIFFRACTIONr_lrange_it5.77628.6484558
X-RAY DIFFRACTIONr_lrange_other5.5427.9774414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3421640.2953227X-RAY DIFFRACTION99.0941
1.847-1.8970.3041640.2413103X-RAY DIFFRACTION99.543
1.897-1.9520.2781660.2253067X-RAY DIFFRACTION99.8764
1.952-2.0120.2611480.213000X-RAY DIFFRACTION99.9048
2.012-2.0780.2941520.2012891X-RAY DIFFRACTION100
2.078-2.1510.2221680.1772760X-RAY DIFFRACTION99.8295
2.151-2.2320.1911340.1652719X-RAY DIFFRACTION99.86
2.232-2.3230.1981380.1532593X-RAY DIFFRACTION99.7079
2.323-2.4270.2041340.1592514X-RAY DIFFRACTION99.8492
2.427-2.5450.2241350.1532384X-RAY DIFFRACTION99.7624
2.545-2.6820.2281250.1552284X-RAY DIFFRACTION99.917
2.682-2.8450.2121250.152150X-RAY DIFFRACTION99.9122
2.845-3.0410.223950.1472051X-RAY DIFFRACTION99.814
3.041-3.2840.173890.1491926X-RAY DIFFRACTION99.9008
3.284-3.5970.195870.1421785X-RAY DIFFRACTION99.8933
3.597-4.0210.17790.1331616X-RAY DIFFRACTION100
4.021-4.640.172760.121428X-RAY DIFFRACTION99.8672
4.64-5.6780.171660.1271247X-RAY DIFFRACTION100
5.678-8.0080.185440.152983X-RAY DIFFRACTION100
8.008-42.0250.147290.161590X-RAY DIFFRACTION98.7241

+
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