[English] 日本語
Yorodumi
- PDB-3upw: Pichia Stipitis OYE2.6 complexed with nicotinamide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3upw
TitlePichia Stipitis OYE2.6 complexed with nicotinamide
ComponentsOld Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase
KeywordsOXIDOREDUCTASE / OYE / old yellow enzyme / FMN / Alkene Reductase / assymetric alkene reduction / OYE1 homologue / TIM Barrel / NADPH Oxidoreductase / NAD(P)H
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
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
FLAVIN MONONUCLEOTIDE / MALONIC ACID / NICOTINAMIDE / NADPH dehydrogenase
Similarity search - Component
Biological speciesScheffersomyces stipitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å
AuthorsPompeu, Y.A. / Stewart, J.D.
CitationJournal: Adv.Synth.Catal. / Year: 2012
Title: Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions
Authors: Pompeu, Y.A. / Sullivan, B. / Walton, A.Z. / Stewart, J.D.
History
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Non-polymer description
Revision 1.2Sep 13, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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: Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,27810
Polymers45,2961
Non-polymers9839
Water8,017445
1
A: Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase
hetero molecules

A: Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,55620
Polymers90,5912
Non-polymers1,96518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5910 Å2
ΔGint-106 kcal/mol
Surface area29580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.306, 127.306, 123.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-526-

HOH

31A-652-

HOH

41A-656-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase


Mass: 45295.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis (fungus) / Strain: ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545 / Gene: OYE2.6, PICST_44614 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A3LT82, NADPH dehydrogenase

-
Non-polymers , 5 types, 454 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M Na Malonate, 2%iPrOH, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.99 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 54454 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 10.7 % / Biso Wilson estimate: 22.44 Å2 / Rsym value: 0.047 / Net I/σ(I): 37.1
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1786 / Rsym value: 0.55 / % possible all: 96

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OYA

1oya


Resolution: 1.781→44.241 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 5649 10 %10% random
Rwork0.1577 ---
obs0.1605 54454 99.76 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.738 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7835 Å20 Å20 Å2
2---0.7835 Å20 Å2
3---1.567 Å2
Refinement stepCycle: LAST / Resolution: 1.781→44.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 65 445 3684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073350
X-RAY DIFFRACTIONf_angle_d1.0494567
X-RAY DIFFRACTIONf_dihedral_angle_d15.0531236
X-RAY DIFFRACTIONf_chiral_restr0.074504
X-RAY DIFFRACTIONf_plane_restr0.004595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7809-1.80120.30321780.28621608X-RAY DIFFRACTION96
1.8012-1.82240.3081840.25041650X-RAY DIFFRACTION98
1.8224-1.84460.27341850.23281665X-RAY DIFFRACTION100
1.8446-1.86790.2331840.19951658X-RAY DIFFRACTION100
1.8679-1.89250.21761850.1911658X-RAY DIFFRACTION100
1.8925-1.91840.2381840.1921662X-RAY DIFFRACTION100
1.9184-1.94580.21841870.18151685X-RAY DIFFRACTION100
1.9458-1.97490.22171840.16921653X-RAY DIFFRACTION100
1.9749-2.00570.20591880.16241689X-RAY DIFFRACTION100
2.0057-2.03860.21211870.15721677X-RAY DIFFRACTION100
2.0386-2.07380.19931830.16331665X-RAY DIFFRACTION100
2.0738-2.11150.18821880.16411680X-RAY DIFFRACTION100
2.1115-2.15210.18041860.15871675X-RAY DIFFRACTION100
2.1521-2.1960.17331880.14841692X-RAY DIFFRACTION100
2.196-2.24380.18221860.14851680X-RAY DIFFRACTION100
2.2438-2.2960.18841880.15781685X-RAY DIFFRACTION100
2.296-2.35340.19391870.15541680X-RAY DIFFRACTION100
2.3534-2.4170.16121860.15181687X-RAY DIFFRACTION100
2.417-2.48810.18371880.15471686X-RAY DIFFRACTION100
2.4881-2.56840.18661900.16061706X-RAY DIFFRACTION100
2.5684-2.66020.18521870.16911689X-RAY DIFFRACTION100
2.6602-2.76670.2091900.18281703X-RAY DIFFRACTION100
2.7667-2.89260.20681890.17471702X-RAY DIFFRACTION100
2.8926-3.04510.20041900.17121710X-RAY DIFFRACTION100
3.0451-3.23580.18861900.15891714X-RAY DIFFRACTION100
3.2358-3.48560.17221900.14331712X-RAY DIFFRACTION100
3.4856-3.83610.16921940.13121739X-RAY DIFFRACTION100
3.8361-4.39080.15081950.11351753X-RAY DIFFRACTION100
4.3908-5.53030.13141980.13081781X-RAY DIFFRACTION100
5.5303-44.25420.19922100.17921891X-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