[English] 日本語
Yorodumi
- PDB-5e9z: Cytochrome P450 BM3 mutant M11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e9z
TitleCytochrome P450 BM3 mutant M11
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / metabolism / molecular dynamics / free energy calculations / thermodynamic integration
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / PROTOPORPHYRIN IX / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsCapoferri, L. / Leth, R. / ter Haar, E. / Mohanty, A.K. / Grootenhuis, D.J. / Vottero, E. / Commandeur, J.N.M. / Vermeulen, N.P.E. / Jorgensen, F.S. / Olsen, L. / Geerke, D.P.
CitationJournal: Proteins / Year: 2016
Title: Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations.
Authors: Capoferri, L. / Leth, R. / Ter Haar, E. / Mohanty, A.K. / Grootenhuis, P.D. / Vottero, E. / Commandeur, J.N. / Vermeulen, N.P. / Jrgensen, F.S. / Olsen, L. / Geerke, D.P.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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.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.value / _pdbx_struct_oper_list.symmetry_operation / _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: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
C: Bifunctional cytochrome P450/NADPH--P450 reductase
D: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,46713
Polymers212,8394
Non-polymers2,6289
Water22,6091255
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8283
Polymers53,2101
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9824
Polymers53,2101
Non-polymers7733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8283
Polymers53,2101
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8283
Polymers53,2101
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)379.122, 59.720, 95.587
Angle α, β, γ (deg.)90.000, 95.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-748-

HOH

-
Components

#1: Protein
Bifunctional cytochrome P450/NADPH--P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3


Mass: 53209.672 Da / Num. of mol.: 4 / Fragment: UNP residues 1-468
Mutation: R47L, E64G, F81I, F87V, E143G, L188Q, Y198C, E267V, H285Y, G415S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1, cyp102 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-PP9 / PROTOPORPHYRIN IX


Mass: 562.658 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34N4O4
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1255 / 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: 2.54 Å3/Da / Density % sol: 51.58 % / Description: orange/red square tiles
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Prior to the crystallization setup, 3mM of DTT was added to the concentrated M11 protein sample. Crystals were grown using hanging drops mixing 0.5 uL of M11 with 0.5 uL of the reservoir ...Details: Prior to the crystallization setup, 3mM of DTT was added to the concentrated M11 protein sample. Crystals were grown using hanging drops mixing 0.5 uL of M11 with 0.5 uL of the reservoir solution containing 10-15% PEG 3350, 0.1M Tris pH8.0, 0.1-0.2 M MgCl2 or MgSO4, and 10 mM DTT

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.2 % / Number: 328643 / Rmerge(I) obs: 0.079 / D res high: 2.22 Å / D res low: 188.63 Å / Num. obs: 101826 / % possible obs: 96.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.222.3410.4982.7
7.01188.6310.0373.4
ReflectionResolution: 2.22→95.12 Å / Num. all: 101826 / Num. obs: 101826 / % possible obs: 96.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 30.88 Å2 / Rpim(I) all: 0.062 / Rrim(I) all: 0.114 / Rsym value: 0.079 / Net I/av σ(I): 7.805 / Net I/σ(I): 9.1 / Num. measured all: 328643
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.22-2.342.70.4981.437951140750.5090.4982.292.1
2.34-2.483.10.2542.843960142880.2130.2543.798.3
2.48-2.653.10.2083.442169133910.1750.2084.897.9
2.65-2.863.30.1534.641294125760.1220.1536.298.5
2.86-3.143.50.1116.340510117180.0830.1117.999.1
3.14-3.513.40.0828.834915102240.060.08212.196.2
3.51-4.053.30.06410.72898186760.0470.06415.792.2
4.05-4.963.50.04813.12680576360.0320.04820.195.1
4.96-7.013.50.04513.92063758840.030.0452094.1
7.01-95.1193.40.03715.51142133580.0250.03722.794.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.52 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.46 Å188.39 Å
Translation3.46 Å188.39 Å

-
Processing

Software
NameVersionClassification
BUSTER-TNTrefinement
SCALA3.3.15data scaling
PHASER2.1.4phasing
Coot0.8.1model building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EKB

3ekb


Resolution: 2.23→95.12 Å / Cor.coef. Fo:Fc: 0.9333 / Cor.coef. Fo:Fc free: 0.9106 / SU R Cruickshank DPI: 0.286 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.304 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.205
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 4824 4.94 %RANDOM
Rwork0.1876 ---
obs0.1895 97560 93.33 %-
Displacement parametersBiso max: 139.49 Å2 / Biso mean: 35.09 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-4.3795 Å20 Å2-1.2663 Å2
2---3.1708 Å20 Å2
3----1.2088 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: final / Resolution: 2.23→95.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14122 0 310 1255 15687
Biso mean--21.06 41.21 -
Num. residues----1792
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5168SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes382HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2283HARMONIC5
X-RAY DIFFRACTIONt_it14802HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1864SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17499SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14802HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg20170HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion18.06
LS refinement shellResolution: 2.23→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5351 203 4.88 %
Rwork0.475 3959 -
all0.4779 4162 -
obs--54.43 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-66.5158-20.958417.901
2-71.71835.849-31.2381
3-19.95711.215123.4797
4-37.7104-28.176973.0935
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|226 A|229 - A|456 A|501 - A|502 A|900 - A|900 }A3 - 226
2X-RAY DIFFRACTION1{ A|3 - A|226 A|229 - A|456 A|501 - A|502 A|900 - A|900 }A229 - 456
3X-RAY DIFFRACTION1{ A|3 - A|226 A|229 - A|456 A|501 - A|502 A|900 - A|900 }A501 - 502
4X-RAY DIFFRACTION1{ A|3 - A|226 A|229 - A|456 A|501 - A|502 A|900 - A|900 }A900
5X-RAY DIFFRACTION2{ B|5 - B|455 B|501 - B|502 }B5 - 455
6X-RAY DIFFRACTION2{ B|5 - B|455 B|501 - B|502 }B501 - 502
7X-RAY DIFFRACTION3{ C|-1 - C|189 C|201 - C|228 C|231 - C|456 C|501 - C|502 }C-1 - 189
8X-RAY DIFFRACTION3{ C|-1 - C|189 C|201 - C|228 C|231 - C|456 C|501 - C|502 }C201 - 228
9X-RAY DIFFRACTION3{ C|-1 - C|189 C|201 - C|228 C|231 - C|456 C|501 - C|502 }C231 - 456
10X-RAY DIFFRACTION3{ C|-1 - C|189 C|201 - C|228 C|231 - C|456 C|501 - C|502 }C501 - 502
11X-RAY DIFFRACTION4{ D|3 - D|189 D|197 - D|225 D|229 - D|456 D|501 - D|502 }D3 - 189
12X-RAY DIFFRACTION4{ D|3 - D|189 D|197 - D|225 D|229 - D|456 D|501 - D|502 }D197 - 225
13X-RAY DIFFRACTION4{ D|3 - D|189 D|197 - D|225 D|229 - D|456 D|501 - D|502 }D229 - 456
14X-RAY DIFFRACTION4{ D|3 - D|189 D|197 - D|225 D|229 - D|456 D|501 - D|502 }D501 - 502

+
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://pdbjlvh1.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