[English] 日本語
Yorodumi
- PDB-3p80: Pentaerythritol tetranitrate reductase co-crystal structure conta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p80
TitlePentaerythritol tetranitrate reductase co-crystal structure containing bound (E)-1-(3'-hydroxyphenyl)-2-nitroethene
ComponentsPentaerythritol tetranitrate reductase
KeywordsOXIDOREDUCTASE / old yellow enzyme family / alpha / beta barrel
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / cytosol
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 / 3-[(E)-2-nitroethenyl]phenol / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsToogood, H.S. / Scrutton, N.S.
CitationJournal: Chembiochem / Year: 2011
Title: A Site-Saturated Mutagenesis Study of Pentaerythritol Tetranitrate Reductase Reveals that Residues 181 and 184 Influence Ligand Binding, Stereochemistry and Reactivity.
Authors: Toogood, H.S. / Fryszkowska, A. / Hulley, M. / Sakuma, M. / Mansell, D. / Stephens, G.M. / Gardiner, J.M. / Scrutton, N.S.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Pentaerythritol tetranitrate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3224
Polymers39,5351
Non-polymers7873
Water12,755708
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.494, 70.642, 88.956
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Pentaerythritol tetranitrate reductase


Mass: 39535.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: PB2 / Gene: onr, PETNR / Plasmid: pBluescript II-KS(+) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P71278, NADPH dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-P80 / 3-[(E)-2-nitroethenyl]phenol / (E)-1-(3'-hydroxyphenyl)-2-nitroethene


Mass: 165.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.2
Details: 100mM sodium cacodylate, 100 mM sodium acetate, 16-18% isopropanol, pH 6.2, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: ADSC Q315 / Detector: CCD / Date: Mar 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.2→55.32 Å / Num. all: 111905 / Num. obs: 111905 / % possible obs: 98.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.2-1.263.30.1724.153475162550.17299.2
1.26-1.343.40.1196.152519154900.11999.6
1.34-1.433.40.0927.850203145760.09299.6
1.43-1.553.50.06410.747226135840.06499.5
1.55-1.73.50.04913.443520125280.04999.5
1.7-1.93.50.04413.939301113500.04499.3
1.9-2.193.50.04213.83447599890.04298.9
2.19-2.683.20.0319.62724285000.0398.8
2.68-3.793.40.02425.12252465710.02497.3
3.79-44.5923.20.02327.9976430620.02379.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å44.59 Å
Translation3 Å44.59 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H50

1h50


Resolution: 1.2→21.21 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1586 / WRfactor Rwork: 0.134 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.916 / SU B: 1.015 / SU ML: 0.021 / SU R Cruickshank DPI: 0.0359 / SU Rfree: 0.0353 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1548 5606 5 %RANDOM
Rwork0.1307 ---
obs0.1319 111821 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.68 Å2 / Biso mean: 11.8041 Å2 / Biso min: 3.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.2→21.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 55 708 3532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223034
X-RAY DIFFRACTIONr_bond_other_d0.0020.022041
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9884158
X-RAY DIFFRACTIONr_angle_other_deg1.3633.0014961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.08123.931145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19515480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6761526
X-RAY DIFFRACTIONr_chiral_restr0.0830.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023506
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02607
X-RAY DIFFRACTIONr_nbd_refined0.2110.2619
X-RAY DIFFRACTIONr_nbd_other0.2220.22379
X-RAY DIFFRACTIONr_nbtor_refined0.180.21502
X-RAY DIFFRACTIONr_nbtor_other0.0790.21611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2490
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.258
X-RAY DIFFRACTIONr_mcbond_it1.2061.51979
X-RAY DIFFRACTIONr_mcbond_other0.7471.5759
X-RAY DIFFRACTIONr_mcangle_it1.52322999
X-RAY DIFFRACTIONr_scbond_it2.11131292
X-RAY DIFFRACTIONr_scangle_it2.8754.51138
X-RAY DIFFRACTIONr_rigid_bond_restr1.16435659
X-RAY DIFFRACTIONr_sphericity_free5.2873708
X-RAY DIFFRACTIONr_sphericity_bonded2.88834994
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 441 -
Rwork0.249 7736 -
all-8177 -
obs--98.91 %

+
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