[English] 日本語
Yorodumi
- PDB-4kvr: Crystal Structure of Prochlorococcus marinus aldehyde-deformylati... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kvr
TitleCrystal Structure of Prochlorococcus marinus aldehyde-deformylating oxygenase (mutant V41Y)
ComponentsAldehyde decarbonylase
KeywordsOXIDOREDUCTASE / Propane production / Aldehyde-deformylating oxygenase
Function / homology
Function and homology information


aldehyde oxygenase (deformylating) activity / aldehyde oxygenase (deformylating) / transition metal ion binding
Similarity search - Function
Long-chain fatty aldehyde decarbonylase / Long-chain fatty aldehyde decarbonylase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEXANOIC ACID / : / Aldehyde decarbonylase
Similarity search - Component
Biological speciesProchlorococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsLevy, C.W. / Khara, B. / Menon, N. / Mansell, D. / Das, D. / Marsh, E.N.G. / Leys, D. / Scrutton, N.S.
CitationJournal: Chembiochem / Year: 2013
Title: Production of propane and other short-chain alkanes by structure-based engineering of ligand specificity in aldehyde-deformylating oxygenase.
Authors: Khara, B. / Menon, N. / Levy, C. / Mansell, D. / Das, D. / Marsh, E.N. / Leys, D. / Scrutton, N.S.
History
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_seq_id / _struct_conn.ptnr2_label_asym_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: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5574
Polymers27,3291
Non-polymers2283
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aldehyde decarbonylase
hetero molecules

A: Aldehyde decarbonylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1148
Polymers54,6582
Non-polymers4566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1770 Å2
ΔGint-1 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.240, 78.240, 117.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Aldehyde decarbonylase / AD / Fatty aldehyde decarbonylase


Mass: 27329.018 Da / Num. of mol.: 1 / Mutation: V41Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus (bacteria) / Strain: MIT 9313 / Gene: PMT_1231 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q7V6D4, aldehyde oxygenase (deformylating)
#2: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M sodium HEPES; MOPS buffer, 0.1M [Na -formate; NH4-acetate; Na3-citrate; Na K-tartrate (racemic); Na- oxamate], ethylene glycol, PEG 8K 30%, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2012
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→55.32 Å / Num. obs: 29998
Reflection shellResolution: 1.88→1.947 Å / % possible all: 99.36

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→55.32 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 23.14 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2183 1520 5.07 %
Rwork0.1917 --
obs0.1931 29995 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→55.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1760 0 10 228 1998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191829
X-RAY DIFFRACTIONf_angle_d1.0862486
X-RAY DIFFRACTIONf_dihedral_angle_d13.424686
X-RAY DIFFRACTIONf_chiral_restr0.069271
X-RAY DIFFRACTIONf_plane_restr0.004323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8801-1.94080.28571420.2622556X-RAY DIFFRACTION99
1.9408-2.01010.26131400.24812576X-RAY DIFFRACTION99
2.0101-2.09060.26351410.232545X-RAY DIFFRACTION99
2.0906-2.18580.26541270.22162588X-RAY DIFFRACTION99
2.1858-2.3010.26171190.20922598X-RAY DIFFRACTION99
2.301-2.44520.26441330.21232578X-RAY DIFFRACTION99
2.4452-2.6340.21931330.2112576X-RAY DIFFRACTION99
2.634-2.8990.23651550.20752564X-RAY DIFFRACTION98
2.899-3.31850.2371550.20612568X-RAY DIFFRACTION98
3.3185-4.18070.21141330.17442623X-RAY DIFFRACTION97
4.1807-55.3480.1711420.16472703X-RAY DIFFRACTION95

+
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