[English] 日本語
Yorodumi
- PDB-4h4i: OYE1-W116V complexed with the dismutation product of (S)-carvone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h4i
TitleOYE1-W116V complexed with the dismutation product of (S)-carvone
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / carvone / dismutation / enantioselectivity / enantiocomplementary / flipped binding / alpha/beta barrel / TIM barrel / nad(P)h oxidoreductase / NAD(P)H / FMN
Function / homology
Function and homology information


: / NADPH dehydrogenase / NADPH dehydrogenase activity / FMN binding
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-methyl-5-(prop-1-en-2-yl)phenol / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPompeu, Y.A. / Stewart, J.D.
CitationJournal: ACS CATALYSIS / Year: 2013
Title: X-ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in an Alkene Reductase
Authors: Pompeu, Y.A. / Sullivan, B. / Stewart, J.D.
History
DepositionSep 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Data collection / Derived calculations
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,03918
Polymers44,9851
Non-polymers2,05517
Water11,890660
1
A: NADPH dehydrogenase 1
hetero molecules

A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,07936
Polymers89,9692
Non-polymers4,10934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9290 Å2
ΔGint-212 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.004, 141.004, 42.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-406-

MG

21A-1043-

HOH

31A-1046-

HOH

41A-1051-

HOH

51A-1086-

HOH

61A-1144-

HOH

71A-1150-

HOH

81A-1154-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein NADPH dehydrogenase 1 / Old yellow enzyme 1


Mass: 44984.562 Da / Num. of mol.: 1 / Mutation: W116V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02899, NADPH dehydrogenase

-
Non-polymers , 7 types, 677 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0WV / 2-methyl-5-(prop-1-en-2-yl)phenol


Mass: 148.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M MgCl2, 35%PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 15, 2011 / Details: Si (111)
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.25→23.6 Å / Num. obs: 119164 / % possible obs: 99.98 % / Observed criterion σ(I): 1 / Redundancy: 10.2 % / Rmerge(I) obs: 0.08 / Rsym value: 0.1 / Net I/σ(I): 19.58
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.916 / Mean I/σ(I) obs: 3.07 / Num. unique all: 9018 / Rsym value: 0.55 / % possible all: 99.95

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RND

3rnd


Resolution: 1.25→23.552 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 11.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1459 11633 10 %random
Rwork0.1235 ---
obs0.1257 116372 97.64 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→23.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 108 660 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013483
X-RAY DIFFRACTIONf_angle_d1.4674732
X-RAY DIFFRACTIONf_dihedral_angle_d16.7631345
X-RAY DIFFRACTIONf_chiral_restr0.139484
X-RAY DIFFRACTIONf_plane_restr0.01618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2499-1.26410.20443670.15823274X-RAY DIFFRACTION93
1.2641-1.2790.16993570.14313300X-RAY DIFFRACTION94
1.279-1.29460.17293640.13863312X-RAY DIFFRACTION93
1.2946-1.3110.16963620.13053276X-RAY DIFFRACTION94
1.311-1.32820.16163770.12043347X-RAY DIFFRACTION94
1.3282-1.34640.16493660.11823361X-RAY DIFFRACTION95
1.3464-1.36560.143750.11273388X-RAY DIFFRACTION96
1.3656-1.3860.15083800.11343392X-RAY DIFFRACTION96
1.386-1.40770.15073750.11313386X-RAY DIFFRACTION96
1.4077-1.43070.15763850.11433407X-RAY DIFFRACTION96
1.4307-1.45540.1523790.11523429X-RAY DIFFRACTION97
1.4554-1.48190.14243840.11813460X-RAY DIFFRACTION98
1.4819-1.51040.15873860.11333440X-RAY DIFFRACTION98
1.5104-1.54120.13263900.10423514X-RAY DIFFRACTION98
1.5412-1.57470.14453890.10273498X-RAY DIFFRACTION99
1.5747-1.61130.13183880.10133484X-RAY DIFFRACTION99
1.6113-1.65160.13863950.10463539X-RAY DIFFRACTION99
1.6516-1.69620.12833870.10783487X-RAY DIFFRACTION99
1.6962-1.74610.13913910.10793534X-RAY DIFFRACTION99
1.7461-1.80250.13183960.11053560X-RAY DIFFRACTION99
1.8025-1.86690.14563990.11433576X-RAY DIFFRACTION100
1.8669-1.94160.1363940.11473568X-RAY DIFFRACTION100
1.9416-2.02990.12773950.11643550X-RAY DIFFRACTION100
2.0299-2.13690.13674020.11553618X-RAY DIFFRACTION100
2.1369-2.27070.13063980.11113585X-RAY DIFFRACTION100
2.2707-2.44580.13473990.1193588X-RAY DIFFRACTION100
2.4458-2.69160.15024050.12683643X-RAY DIFFRACTION100
2.6916-3.08040.15034070.13693662X-RAY DIFFRACTION100
3.0804-3.87810.14814110.13573701X-RAY DIFFRACTION100
3.8781-23.55580.16214300.15273860X-RAY DIFFRACTION100

+
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