[English] 日本語
Yorodumi
- PDB-5l94: The 2.25 A crystal structure of CYP109E1 from Bacillus megaterium... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l94
TitleThe 2.25 A crystal structure of CYP109E1 from Bacillus megaterium in complex with testosterone
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Bacillus / Bacterial Proteins / Binding Sites / Catalysis / Cytochrome P-450 Enzyme System / Cytochrome P450 / Hydroxylation / Escherichia coli / Heme / Ligands / Molecular Structure / Oxidation-Reduction / Oxygen / Protein / Protein Structure / Secondary / Steroids / Substrate Specificity / Testosterone
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / TESTOSTERONE / Cytochrome P450
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsJozwik, I.K. / Thunnissen, A.M.W.H.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission289217 Netherlands
CitationJournal: Febs J. / Year: 2016
Title: Structural basis of steroid binding and oxidation by the cytochrome P450 CYP109E1 from Bacillus megaterium.
Authors: Jozwik, I.K. / Kiss, F.M. / Abdulmughni, A. / Brill, E. / Zapp, J. / Pleiss, J. / Bernhardt, R. / Thunnissen, A.W.
History
DepositionJun 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1585
Polymers95,6372
Non-polymers1,5213
Water4,378243
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7233
Polymers47,8181
Non-polymers9052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4352
Polymers47,8181
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.359, 134.922, 61.870
Angle α, β, γ (deg.)90.000, 113.830, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cytochrome P450


Mass: 47818.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (strain DSM 319) (bacteria)
Strain: DSM 319 / Gene: BMD_3874 / Production host: Escherichia coli (E. coli)
References: UniProt: D5DKI8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: D5DKI8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 9% PEG 3350 and 8% tacsimate pH 5.0

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 19, 2015 / Details: HELIOS OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→56.59 Å / Num. obs: 42810 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.53 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.157 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.25-2.326.80.803199.1
9-56.596.50.034199.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.25 Å56.59 Å
Translation2.25 Å56.59 Å

-
Processing

Software
NameVersionClassification
MOSFLMdata collection
XDSdata reduction
Aimless0.5.1data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ggv

4ggv


Resolution: 2.25→56.59 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 29.85
RfactorNum. reflection% reflection
Rfree0.2628 4284 5.07 %
Rwork0.219 --
obs0.2213 42810 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.63 Å2 / Biso mean: 36.3872 Å2 / Biso min: 18.75 Å2
Refinement stepCycle: final / Resolution: 2.25→56.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 107 243 6444
Biso mean--26.47 33.94 -
Num. residues----745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146352
X-RAY DIFFRACTIONf_angle_d1.2528617
X-RAY DIFFRACTIONf_chiral_restr0.057928
X-RAY DIFFRACTIONf_plane_restr0.0081101
X-RAY DIFFRACTIONf_dihedral_angle_d16.2912418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.27560.57211760.52692663283999
2.2756-2.30230.40931460.37652632277899
2.3023-2.33040.44631340.35712624275899
2.3304-2.35990.32621650.31432689285499
2.3599-2.3910.36581520.29982647279999
2.391-2.42370.33731890.28312603279299
2.4237-2.45840.35661260.28412677280399
2.4584-2.49510.3441560.28226702826100
2.4951-2.5340.33891230.30552643276699
2.534-2.57560.34331360.263527272863100
2.5756-2.620.31091080.2652679278799
2.62-2.66760.33741240.252826752799100
2.6676-2.71890.34811330.253926912824100
2.7189-2.77440.21071330.256127552888100
2.7744-2.83480.28991270.261326492776100
2.8348-2.90070.29331410.237526882829100
2.9007-2.97320.24071470.233526682815100
2.9732-3.05360.30561550.224226332788100
3.0536-3.14350.27821770.231226942871100
3.1435-3.24490.28891380.227126742812100
3.2449-3.36090.22021460.200926842830100
3.3609-3.49540.26631230.205626752798100
3.4954-3.65450.26621420.217727032845100
3.6545-3.84710.23161390.199226792818100
3.8471-4.08810.19811550.173826652820100
4.0881-4.40360.20171260.143727072833100
4.4036-4.84660.15731460.145126532799100
4.8466-5.54740.18651670.151326792846100
5.5474-6.9870.22651250.1726712796100
6.987-56.6120.18351290.14272640276997

+
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