[English] 日本語
Yorodumi
- PDB-8sby: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sby
TitleCrystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (NAD and sulfate bound, hexagonal form)
Components2,3-dihydroxybenzoate-2,3-dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase / 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase activity / siderophore biosynthetic process / nucleotide binding
Similarity search - Function
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase / PKS_KR / 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 domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (NAD and sulfate bound, hexagonal form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionApr 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2,3-dihydroxybenzoate-2,3-dehydrogenase
B: 2,3-dihydroxybenzoate-2,3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,40815
Polymers55,1462
Non-polymers2,26213
Water93752
1
A: 2,3-dihydroxybenzoate-2,3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6216
Polymers27,5731
Non-polymers1,0485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2,3-dihydroxybenzoate-2,3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7889
Polymers27,5731
Non-polymers1,2158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.312, 126.312, 105.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein 2,3-dihydroxybenzoate-2,3-dehydrogenase


Mass: 27572.984 Da / Num. of mol.: 2 / Mutation: A2N, A3G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: EAE_13665 / Plasmid: KlaeA.01365.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FXS4
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 2.0 M Ammonium Sulfate, 0.1 M Cacodylate 6.4. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. 2mM NAD added to the protein prior to crystallization. Plate: liu-S-077 well G8, Puck: PSL-0612, Cryo: 2.5 M lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→109.39 Å / Num. obs: 22669 / % possible obs: 100 % / Redundancy: 39.3 % / CC1/2: 1 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.015 / Rrim(I) all: 0.097 / Χ2: 0.99 / Net I/σ(I): 29.3 / Num. measured all: 891424
Reflection shellResolution: 2.3→2.36 Å / % possible obs: 100 % / Redundancy: 42.1 % / Rmerge(I) obs: 2.203 / Num. measured all: 68846 / Num. unique obs: 1635 / CC1/2: 0.811 / Rpim(I) all: 0.34 / Rrim(I) all: 2.23 / Χ2: 0.96 / Net I/σ(I) obs: 2.2

-
Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4918: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 1100 4.86 %
Rwork0.1778 --
obs0.1811 22622 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 135 52 3703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113704
X-RAY DIFFRACTIONf_angle_d1.1155042
X-RAY DIFFRACTIONf_dihedral_angle_d14.3061254
X-RAY DIFFRACTIONf_chiral_restr0.053578
X-RAY DIFFRACTIONf_plane_restr0.011648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.30641400.2212618X-RAY DIFFRACTION100
2.4-2.530.33641340.20322644X-RAY DIFFRACTION100
2.53-2.690.24741430.20472634X-RAY DIFFRACTION100
2.69-2.90.28861270.21412657X-RAY DIFFRACTION100
2.9-3.190.26721320.22262670X-RAY DIFFRACTION100
3.19-3.650.24951340.1952693X-RAY DIFFRACTION100
3.65-4.60.21951430.14962726X-RAY DIFFRACTION100
4.6-380.22941470.16082880X-RAY DIFFRACTION100
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)
10.3578-0.30240.14520.5878-0.20340.63710.095-0.2070.39340.2309-0.20410.3758-0.2669-0.146800.6089-0.0780.07850.4759-0.15120.6075-13.562466.461217.0239
20.4152-0.54590.12411.7863-0.05620.23480.1165-0.15560.15880.1713-0.18290.16940.1046-0.1256-0.00010.5184-0.07010.00410.4957-0.06230.5182-10.993652.409512.4251
30.98750.4456-0.03060.79920.46960.38770.061-0.06360.26360.2158-0.2091-0.13210.0234-0.03980.00020.5068-0.0654-0.0260.4386-0.0010.54655.123455.14878.7905
40.69230.31330.30041.2266-0.68390.76980.1836-0.1614-0.17670.3283-0.15390.09870.3249-0.247800.649-0.128-0.00810.4980.01620.517-13.624718.073816.8566
50.5607-0.91260.01021.4566-0.0134-0.01310.1539-0.0975-0.03720.2651-0.23190.19460.0189-0.0775-0.00010.5665-0.116-0.00280.4432-0.03070.4596-9.816732.772114.7376
60.61830.3319-0.44780.4223-0.39180.4190.19080.09910.0267-0.2293-0.173-0.03190.2198-0.0652-0.00010.5812-0.0158-0.08420.4888-0.070.4857-9.932329.1453-1.2268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 193 )
3X-RAY DIFFRACTION3chain 'A' and (resid 194 through 251 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 70 )
5X-RAY DIFFRACTION5chain 'B' and (resid 71 through 168 )
6X-RAY DIFFRACTION6chain 'B' and (resid 169 through 251 )

+
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