[English] 日本語
Yorodumi
- PDB-8hr6: leucine DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hr6
Titleleucine DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ from Bacillus thuringiensis
ComponentsLeucine dehydrogenase
KeywordsOXIDOREDUCTASE / leucine DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ from Bacillus thuringiensis
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsLi, X. / Song, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2023
Title: A Tri-Enzyme Cascade for Efficient Production of L-2-Aminobutyrate from L-Threonine.
Authors: Li, X. / Gao, C. / Wei, W. / Song, W. / Meng, W. / Liu, J. / Chen, X. / Gao, C. / Guo, L. / Liu, L. / Wu, J.
History
DepositionDec 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine dehydrogenase
B: Leucine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,11515
Polymers79,7322
Non-polymers2,38413
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-157 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.434, 121.434, 178.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

-
Components

#1: Protein Leucine dehydrogenase / Leucine dehydrogenase Ldh


Mass: 39865.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria)
Gene: ldh1, BK774_17255, BK775_32270, BTGOE4_46100, BUM91_06765, C5676_00473, D7J84_18335, GH851_02505, GH891_02550
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G3E5D9, leucine dehydrogenase
#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.: 11 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% glycerol, 3.75% isopropanol, 1.5M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.52→30.79 Å / Num. obs: 17215 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 0.995 / Net I/σ(I): 7.8
Reflection shellResolution: 3.52→3.85 Å / Num. unique obs: 4016 / CC1/2: 0.948

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5refinement
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→30.79 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.875 / SU B: 63.832 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27867 860 5 %RANDOM
Rwork0.22953 ---
obs0.232 16295 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å2-0 Å2-0 Å2
2--1.39 Å20 Å2
3----2.78 Å2
Refinement stepCycle: 1 / Resolution: 3.52→30.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5470 0 143 3 5616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135691
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155343
X-RAY DIFFRACTIONr_angle_refined_deg1.381.6437719
X-RAY DIFFRACTIONr_angle_other_deg1.1241.58412293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0195710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1522.784291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75215951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4311536
X-RAY DIFFRACTIONr_chiral_restr0.0490.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021229
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7034.8292854
X-RAY DIFFRACTIONr_mcbond_other1.7034.8292853
X-RAY DIFFRACTIONr_mcangle_it3.0147.2363559
X-RAY DIFFRACTIONr_mcangle_other3.0147.2373560
X-RAY DIFFRACTIONr_scbond_it1.4255.2822836
X-RAY DIFFRACTIONr_scbond_other1.3735.1522793
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5357.6884094
X-RAY DIFFRACTIONr_long_range_B_refined8.27858.0556176
X-RAY DIFFRACTIONr_long_range_B_other8.19958.0536175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10851 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.53→3.608 Å
RfactorNum. reflection% reflection
Rfree0.43 64 -
Rwork0.319 1164 -
obs--98.48 %
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)
12.06750.06220.43661.34020.15250.7683-0.01160.1073-0.2348-0.0342-0.007-0.09620.09580.00440.01870.40650.05510.02950.3138-0.03750.27139.866231.194738.2522
20.148-0.1964-0.66110.28651.0424.12320.03390.15650.00920.0282-0.15510.02710.1978-0.24330.12120.32910.08330.16870.4384-0.07290.247722.48831.945212.1118
37.83991.5594-2.69516.3314-0.27874.3324-0.0043-0.42560.0135-0.0237-0.1065-0.59290.5614-0.04390.11080.2730.12250.06880.3806-0.06510.157634.296325.844823.7631
41.3012-0.9542-1.72670.70161.28412.47890.0126-0.0815-0.032-0.03390.06730.0154-0.25060.2041-0.07990.41550.04270.05640.35030.00260.326424.690945.176230.8438
51.8908-1.3281-0.0771.8488-0.49550.3368-0.2096-0.1368-0.18070.17480.16480.0159-0.0117-0.02310.04480.41820.02780.00910.37390.07470.25787.013531.470362.5529
61.37972.81850.12655.7860.17030.52620.2143-0.1471-0.170.5654-0.2137-0.321-0.3544-0.0422-0.00060.61030.39210.10150.52630.19680.0847-4.173126.849589.2157
72.46920.18911.33380.10190.0470.83930.2612-0.14850.2626-0.0019-0.23510.0470.29930.0438-0.02610.49330.0611-0.10240.5916-0.02390.38725.637223.835393.7163
87.45640.11624.50214.5806-1.11623.0389-1.10740.088-1.34780.38651.91910.2276-0.7524-0.3854-0.81170.26850.27580.34131.02050.30710.4689-2.52513.690781.2392
92.67541.488-0.80587.7705-0.8510.3339-0.6286-0.2239-0.04390.00360.76510.00190.0913-0.0768-0.13650.34780.07090.10150.41430.26840.3163-9.397731.830274.021
101.4354-0.87281.46730.7744-1.26462.16490.076-0.4325-0.0724-0.42170.24820.10150.5709-0.4078-0.32420.6332-0.0350.04270.34030.09290.3239-12.660233.527258.8197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 131
2X-RAY DIFFRACTION2A132 - 263
3X-RAY DIFFRACTION3A264 - 284
4X-RAY DIFFRACTION4A285 - 365
5X-RAY DIFFRACTION5B3 - 168
6X-RAY DIFFRACTION6B169 - 197
7X-RAY DIFFRACTION7B198 - 218
8X-RAY DIFFRACTION8B219 - 277
9X-RAY DIFFRACTION9B278 - 328
10X-RAY DIFFRACTION10B329 - 365

+
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