[English] 日本語
Yorodumi
- PDB-9jmy: Crystal structure of IRED in complex with NADPH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jmy
TitleCrystal structure of IRED in complex with NADPH
Components3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / imine reductase
Function / homology
Function and homology information


organic acid catabolic process / NADP binding / oxidoreductase activity
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesAmycolatopsis thermoflava (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFu, X.L. / Zhang, M.T. / Yi, S.M. / Dai, K.X. / Yang, Y.Y. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0911400 China
CitationJournal: To Be Published
Title: Crystal structure of IRED in complex with NADPH
Authors: Fu, X.L. / Zhang, M.T. / Yi, S.M. / Dai, K.X. / Yang, Y.Y. / Chen, C.-C. / Guo, R.-T.
History
DepositionSep 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3659
Polymers60,3932
Non-polymers1,9737
Water3,351186
1
A: 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
hetero molecules

A: 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,73118
Polymers120,7854
Non-polymers3,94614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area29810 Å2
ΔGint-231 kcal/mol
Surface area35120 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-87 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.831, 75.831, 157.008
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-305-

CA

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase / IRED


Mass: 30196.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis thermoflava (bacteria) / Gene: EDD35_0917 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3N2GPT5

-
Non-polymers , 6 types, 193 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 0.03 M CaCl2, 0.1M MES pH 6.0, 49% v/v PEG 200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Oct 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.15→36.88 Å / Num. obs: 29044 / % possible obs: 99.3 % / Redundancy: 5.64 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.12
Reflection shellResolution: 2.15→2.18 Å / Redundancy: 3.14 % / Rmerge(I) obs: 0.2127 / Num. unique obs: 1159 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata scaling
SAINTdata reduction
PDB_EXTRACT2.34data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→36.88 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.549 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24301 1288 4.6 %RANDOM
Rwork0.17449 ---
obs0.17744 27005 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.908 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.15→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 125 186 4519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174111
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.6416033
X-RAY DIFFRACTIONr_angle_other_deg1.3431.5689457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66720.874206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72515640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7841534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02934
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_it1.8412.7242270
X-RAY DIFFRACTIONr_mcbond_other1.8412.7232269
X-RAY DIFFRACTIONr_mcangle_it2.684.0792834
X-RAY DIFFRACTIONr_mcangle_other2.6794.0792835
X-RAY DIFFRACTIONr_scbond_it2.3292.9952148
X-RAY DIFFRACTIONr_scbond_other2.3262.9942146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5394.3763200
X-RAY DIFFRACTIONr_long_range_B_refined4.87333.0684980
X-RAY DIFFRACTIONr_long_range_B_other4.87333.0674981
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 93 -
Rwork0.213 1739 -
obs--86.33 %

+
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