[English] 日本語
Yorodumi
- PDB-4d3s: Imine reductase from Nocardiopsis halophila -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d3s
TitleImine reductase from Nocardiopsis halophila
ComponentsIMINE REDUCTASE
KeywordsOXIDOREDUCTASE / NADPH
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / NADP binding
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesNOCARDIOPSIS HALOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsMan, H. / Hart, S. / Turkenburg, J.P. / Grogan, G.
CitationJournal: Chembiochem / Year: 2015
Title: Structure, Activity and Stereoselectivity of Nadph-Dependent Oxidoreductases Catalysing the S-Selective Reduction of the Imine Substrate 2-Methylpyrroline.
Authors: Man, H. / Wells, E. / Hussain, S. / Leipold, F. / Hart, S. / Turkenburg, J.P. / Turner, N.J. / Grogan, G.
History
DepositionOct 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IMINE REDUCTASE
B: IMINE REDUCTASE
C: IMINE REDUCTASE
D: IMINE REDUCTASE
E: IMINE REDUCTASE
F: IMINE REDUCTASE
G: IMINE REDUCTASE
H: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,64610
Polymers246,0618
Non-polymers5852
Water9,134507
1
D: IMINE REDUCTASE
E: IMINE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)61,5152
Polymers61,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-79.2 kcal/mol
Surface area20970 Å2
MethodPISA
2
C: IMINE REDUCTASE
F: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8083
Polymers61,5152
Non-polymers2921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-75.9 kcal/mol
Surface area20620 Å2
MethodPISA
3
A: IMINE REDUCTASE
H: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8083
Polymers61,5152
Non-polymers2921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-76.3 kcal/mol
Surface area20890 Å2
MethodPISA
4
B: IMINE REDUCTASE
G: IMINE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)61,5152
Polymers61,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-75.5 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.170, 153.920, 105.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.89, -0.1833, 0.4174), (0.05344, 0.9512, 0.3038), (-0.4527, -0.2481, 0.8564)-16.52, 3.958, 117.5
2given(-0.9978, 0.04962, 0.04502), (-0.04934, -0.9988, 0.007277), (0.04532, 0.00504, 0.999)137.7, 79.55, 49.97
3given(-0.8935, -0.1783, -0.4121), (-0.04142, 0.9466, -0.3197), (0.4471, -0.2686, -0.8532)238.9, 63.52, 157.6
4given(-0.4849, 0.5193, 0.7037), (-0.3633, -0.8515, 0.3781), (0.7956, -0.07229, 0.6015)58.31, 68.89, -40.04
5given(-0.1062, -0.2705, -0.9568), (-0.31, 0.9233, -0.2266), (0.9448, 0.2726, -0.1819)160.6, 49.62, 65.75
6given(0.4809, 0.4922, -0.7256), (0.3458, -0.867, -0.3589), (-0.8057, -0.07833, -0.5872)68.97, 52.11, 225
7given(0.07172, 0.2796, -0.9574), (0.3303, -0.9124, -0.2417), (-0.9411, -0.2989, -0.1578)177.3, 88.36, 228.7

-
Components

#1: Protein
IMINE REDUCTASE


Mass: 30757.660 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NOCARDIOPSIS HALOPHILA (bacteria) / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0J9X1X6*PLUS, dihydrofolate reductase
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsN-OCTYL-BETA-D-GLUCOPYRANOSIDE: CRYSTALLISATION ADDITIVE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 5.5
Details: 18% (W/V) PEG 3350; 0. 2 M MGCL2; 0.1M BIS-TRIS PROPANE PH 5.5; 1% (W/V) N-OCTYL-BETA-D-OCTYLPYRANOSIDE

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.39→67.57 Å / Num. obs: 94683 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 2.39→2.47 Å / Redundancy: 7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZGY

3zgy


Resolution: 2.24→67.57 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.948 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26577 5458 4.9 %RANDOM
Rwork0.2302 ---
obs0.23199 94683 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.319 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--2.03 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.24→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15838 0 40 507 16385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01916198
X-RAY DIFFRACTIONr_bond_other_d0.010.0214947
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.96522063
X-RAY DIFFRACTIONr_angle_other_deg1.8813.00234145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02952216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59523.172580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.631152203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9861596
X-RAY DIFFRACTIONr_chiral_restr0.0980.22574
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02118832
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023572
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_it4.0535.0078917
X-RAY DIFFRACTIONr_mcbond_other4.0535.0078916
X-RAY DIFFRACTIONr_mcangle_it5.9587.49311114
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1945.0037281
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 418 -
Rwork0.326 7692 -
obs--99.98 %

+
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