[English] 日本語
Yorodumi
- PDB-4jx1: Crystal structure of reduced Cytochrome P450cam-putidaredoxin com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jx1
TitleCrystal structure of reduced Cytochrome P450cam-putidaredoxin complex bound to camphor and 5-exo-hydroxycamphor
Components
  • Camphor 5-monooxygenase
  • Putidaredoxin
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / reduced P450cam-Pdx complex / redox partners / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


P450-containing electron transport chain / camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / 2 iron, 2 sulfur cluster binding / electron transfer activity / iron ion binding / heme binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Cytochrome P450, B-class / Beta-grasp domain superfamily / Cytochrome p450 / Cytochrome P450 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Cytochrome P450, B-class / Beta-grasp domain superfamily / Cytochrome p450 / Cytochrome P450 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione / 5-EXO-HYDROXYCAMPHOR / CAMPHOR / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase / Putidaredoxin
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.087 Å
AuthorsTripathi, S.M. / Li, H. / Poulos, T.L.
CitationJournal: Science / Year: 2013
Title: Structural basis for effector control and redox partner recognition in cytochrome P450.
Authors: Tripathi, S. / Li, H. / Poulos, T.L.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Camphor 5-monooxygenase
B: Camphor 5-monooxygenase
C: Putidaredoxin
D: Putidaredoxin
E: Camphor 5-monooxygenase
F: Camphor 5-monooxygenase
G: Putidaredoxin
H: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,55828
Polymers235,8358
Non-polymers4,72320
Water35,0931948
1
A: Camphor 5-monooxygenase
C: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1127
Polymers58,9592
Non-polymers1,1535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Camphor 5-monooxygenase
D: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9436
Polymers58,9592
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Camphor 5-monooxygenase
G: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3928
Polymers58,9592
Non-polymers1,4336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Camphor 5-monooxygenase
H: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1127
Polymers58,9592
Non-polymers1,1535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.850, 108.960, 115.160
Angle α, β, γ (deg.)90.00, 109.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 8 molecules ABEFCDGH

#1: Protein
Camphor 5-monooxygenase / Cytochrome P450-cam / Cytochrome P450cam


Mass: 46597.715 Da / Num. of mol.: 4 / Mutation: K344C, C334A, C59S, C86S, C137S, C286S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase
#2: Protein
Putidaredoxin / PDX


Mass: 12360.977 Da / Num. of mol.: 4 / Mutation: C85S, C73S, D19C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00259

-
Non-polymers , 7 types, 1968 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16O
#5: Chemical ChemComp-CAH / 5-EXO-HYDROXYCAMPHOR


Mass: 168.233 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16O2
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-1N0 / 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione / bis(maleimido)hexane, bound form


Mass: 280.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N2O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1948 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.09 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09 Å / Relative weight: 1
ReflectionResolution: 2.087→57.2 Å / Num. obs: 118774 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 15.3
Reflection shellResolution: 2.087→2.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 7.9 / Rsym value: 0.159 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2CPP AND 1XLO

2cpp

1xlo


Resolution: 2.087→44.87 Å / SU ML: 0.2 / σ(F): 1.37 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 5959 5.02 %
Rwork0.1438 --
obs0.1472 118733 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.087→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15972 0 292 1948 18212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01216694
X-RAY DIFFRACTIONf_angle_d1.51922787
X-RAY DIFFRACTIONf_dihedral_angle_d14.2256171
X-RAY DIFFRACTIONf_chiral_restr0.082487
X-RAY DIFFRACTIONf_plane_restr0.0072987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.087-2.11070.24632050.15353600X-RAY DIFFRACTION96
2.1107-2.13550.21182100.13943785X-RAY DIFFRACTION99
2.1355-2.16160.21851800.13783748X-RAY DIFFRACTION99
2.1616-2.18890.23341870.13773760X-RAY DIFFRACTION99
2.1889-2.21770.23462120.13113762X-RAY DIFFRACTION99
2.2177-2.24810.18431720.12653753X-RAY DIFFRACTION99
2.2481-2.28020.2132020.12953762X-RAY DIFFRACTION99
2.2802-2.31430.22131870.13153733X-RAY DIFFRACTION99
2.3143-2.35040.20841890.13443800X-RAY DIFFRACTION99
2.3504-2.3890.23381890.13193754X-RAY DIFFRACTION99
2.389-2.43020.22652040.13383747X-RAY DIFFRACTION99
2.4302-2.47430.21541960.1343788X-RAY DIFFRACTION99
2.4743-2.52190.21341870.1423743X-RAY DIFFRACTION99
2.5219-2.57340.24271960.14673794X-RAY DIFFRACTION99
2.5734-2.62930.24731960.14613781X-RAY DIFFRACTION99
2.6293-2.69050.22782100.1493729X-RAY DIFFRACTION99
2.6905-2.75780.21652250.14123743X-RAY DIFFRACTION99
2.7578-2.83230.22312140.14243786X-RAY DIFFRACTION99
2.8323-2.91570.22791970.14793762X-RAY DIFFRACTION99
2.9157-3.00980.22062090.14653769X-RAY DIFFRACTION99
3.0098-3.11730.22232150.15143778X-RAY DIFFRACTION99
3.1173-3.24210.22082230.1593763X-RAY DIFFRACTION99
3.2421-3.38960.22992010.14713744X-RAY DIFFRACTION99
3.3896-3.56820.19272020.14413761X-RAY DIFFRACTION99
3.5682-3.79170.20171940.13993813X-RAY DIFFRACTION99
3.7917-4.08420.19292020.14463772X-RAY DIFFRACTION99
4.0842-4.49490.17211930.12773799X-RAY DIFFRACTION99
4.4949-5.14450.18481950.13313751X-RAY DIFFRACTION97
5.1445-6.47850.22861690.16813598X-RAY DIFFRACTION93
6.4785-44.88080.18881980.17483896X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7629-0.10260.1460.7972-0.01721.02170.03480.00440.0523-0.0813-0.0632-0.0364-0.0269-0.02080.0280.1182-0.0060.02170.0920.01020.1017-86.83377.41693.4382
21.55170.1905-0.11190.71740.01260.880.0394-0.1541-0.15640.0797-0.05150.05240.0669-0.15920.00860.1333-0.0138-0.01260.18760.05250.1545-43.716723.2803-4.0589
32.07170.3625-0.49732.761-1.15162.57920.0951-0.2385-0.19640.1419-0.12150.12010.2397-0.08090.04890.1875-0.04790.0260.14980.03270.141-88.6907-17.965616.6109
41.9261-0.60730.542.9987-0.89373.5485-0.14150.14870.3808-0.1335-0.02370.1007-0.3631-0.04220.15370.18520.0046-0.05380.19870.06360.2352-45.528648.2172-17.8351
51.0151-0.2653-0.12180.7653-0.05610.9104-0.0265-0.01750.03660.04180.0234-0.0083-0.0388-0.03580.00350.13110.0040.01850.09630.00110.0933-105.39286.096658.5827
60.82890.21960.16640.69890.20110.9235-0.0121-0.0118-0.034-0.0052-0.04030.00290.05440.01180.05560.11290.0098-0.0030.11540.0150.1201-62.021321.498750.9564
72.80190.8177-0.27593.21340.09443.8986-0.0008-0.1002-0.25310.09960.03190.1140.1642-0.1439-0.02110.12590.0180.00820.1330.04310.1679-107.787-20.359368.9855
81.6198-0.68580.90.41-0.45972.1126-0.14640.32710.4352-0.53470.24790.4846-0.393-0.2085-0.02880.4235-0.0475-0.15730.25880.12620.3892-64.268746.406336.9462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:414)
2X-RAY DIFFRACTION2(chain B and resid 10:414)
3X-RAY DIFFRACTION3(chain C and resid 1:106)
4X-RAY DIFFRACTION4(chain D and resid 1:106)
5X-RAY DIFFRACTION5(chain E and resid 10:414)
6X-RAY DIFFRACTION6(chain F and resid 10:414)
7X-RAY DIFFRACTION7(chain G and resid 1:106)
8X-RAY DIFFRACTION8(chain H and resid 1:106)

+
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