[English] 日本語
Yorodumi
- PDB-4l4c: Structure of L358P/K178G mutant of P450cam bound to camphor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l4c
TitleStructure of L358P/K178G mutant of P450cam bound to camphor
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / mono-oxygenase / cytochrome P450
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm
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
CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / : / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBatabyal, D. / Li, H. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2013
Title: Synergistic Effects of Mutations in Cytochrome P450cam Designed To Mimic CYP101D1.
Authors: Batabyal, D. / Li, H. / Poulos, T.L.
History
DepositionJun 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
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.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_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: Camphor 5-monooxygenase
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8549
Polymers93,2002
Non-polymers1,6557
Water9,800544
1
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4475
Polymers46,6001
Non-polymers8474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4084
Polymers46,6001
Non-polymers8083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.581, 61.519, 94.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 46599.840 Da / Num. of mol.: 2 / Mutation: C334A, L358P, K178G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Production host: Escherichia coli (E. coli) / References: UniProt: P00183, camphor 5-monooxygenase
#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-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 50 mM Tris, 400 mM potassium chloride, 32% PEG4000, 1.2 mM D-camphor, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 27, 2012
RadiationMonochromator: VariMax optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 37084 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.4 / % possible all: 68

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CPP

2cpp


Resolution: 2.2→29.263 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 1846 4.98 %
Rwork0.17 --
obs0.1738 37065 93.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 111 544 7057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086686
X-RAY DIFFRACTIONf_angle_d1.2369128
X-RAY DIFFRACTIONf_dihedral_angle_d16.2222490
X-RAY DIFFRACTIONf_chiral_restr0.081976
X-RAY DIFFRACTIONf_plane_restr0.0051204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.25980.2626840.19771605X-RAY DIFFRACTION56
2.2598-2.32630.32551140.18332330X-RAY DIFFRACTION81
2.3263-2.40130.27241380.17512663X-RAY DIFFRACTION92
2.4013-2.48710.27441300.18562720X-RAY DIFFRACTION93
2.4871-2.58660.28361430.18622720X-RAY DIFFRACTION94
2.5866-2.70430.28751300.19272803X-RAY DIFFRACTION96
2.7043-2.84680.27841450.20822862X-RAY DIFFRACTION99
2.8468-3.02490.29351540.21082873X-RAY DIFFRACTION99
3.0249-3.25820.29221710.18682902X-RAY DIFFRACTION100
3.2582-3.58560.23011660.17382875X-RAY DIFFRACTION100
3.5856-4.10320.20821600.14492917X-RAY DIFFRACTION100
4.1032-5.1650.18341500.12462959X-RAY DIFFRACTION100
5.165-29.26520.17331610.14062990X-RAY DIFFRACTION100
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)
11.8992-0.15070.05031.33950.41532.8099-0.05580.22120.0337-0.060.0096-0.086-0.05990.2640.05660.0968-0.0151-0.00040.11060.01870.1289-12.17426.7226-63.0198
21.98120.2015-1.29681.1680.56985.40140.02980.10850.01520.0181-0.06510.2924-0.2231-0.4053-0.01490.1181-0.005-0.02130.08170.00280.1981-32.70928.2616-53.68
37.9185-3.90245.21865.0592-3.09145.2165-0.3024-0.93490.07120.7034-0.07520.3387-0.6426-0.70070.21460.2992-0.06020.02970.3872-0.11490.1786-21.26367.5209-25.613
41.62490.28760.80071.21940.16211.06870.0392-0.1733-0.17720.0794-0.00220.0530.0089-0.1141-0.05640.1238-0.00590.01230.10630.01520.1542-27.8609-0.5922-41.4816
50.75630.0783-0.00350.45820.13211.8902-0.0253-0.03140.11280.082-0.0658-0.0758-0.27810.16420.10040.1591-0.0304-0.02020.0941-0.00280.1595-12.961314.7321-46.575
62.3793-0.08822.35971.0738-0.98034.40640.250.0511-0.12190.2571-0.0301-0.2380.30830.3739-0.20260.1881-0.0115-0.05530.15940.02920.1891-4.98731.0739-33.0307
70.7773-0.3085-0.31861.0857-0.2112.5226-0.1318-0.3063-0.01910.28210.15450.25660.0068-0.5476-0.02960.23730.04170.05020.3730.01070.1679-24.6145-23.703810.3357
81.9069-0.09-1.34290.3892-1.1136.4809-0.0119-0.16940.19290.0817-0.1738-0.2952-0.48180.33770.12520.1976-0.0119-0.03660.13320.01590.2641-1.9145-21.07562.0929
91.0349-0.91431.37240.878-0.9312.75660.17630.0987-0.0179-0.0989-0.0538-0.03020.42870.0972-0.11640.17940.0096-0.00540.1186-0.00360.157-6.7189-32.6462-12.3528
105.495-1.42452.25551.2482-0.65551.19430.0945-0.1323-0.09530.080.0433-0.08620.0064-0.0729-0.08850.1618-0.01460.03550.15950.02370.1146-2.2491-25.4623-5.1342
110.8256-0.0442-0.25220.8606-0.55222.235-0.1265-0.14220.1110.20720.14720.0712-0.3565-0.3758-0.04870.16890.04210.01870.1884-0.02390.1665-22.8703-15.6183-2.1168
121.37280.16831.54790.66990.37493.3007-0.05990.11110.1441-0.0011-0.076-0.0528-0.44480.02910.08170.17150.0079-0.00110.12770.01770.12-14.5084-14.7949-11.4784
132.56070.43911.99481.14651.09322.08160.0049-0.1815-0.0849-0.1817-0.00430.02060.6659-0.6703-0.06040.1922-0.0620.00110.2470.0010.1523-24.9953-28.2027-20.5463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 145 )
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 266 )
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 377 )
6X-RAY DIFFRACTION6chain 'A' and (resid 378 through 414 )
7X-RAY DIFFRACTION7chain 'B' and (resid 10 through 89 )
8X-RAY DIFFRACTION8chain 'B' and (resid 90 through 127 )
9X-RAY DIFFRACTION9chain 'B' and (resid 128 through 213 )
10X-RAY DIFFRACTION10chain 'B' and (resid 214 through 265 )
11X-RAY DIFFRACTION11chain 'B' and (resid 266 through 340 )
12X-RAY DIFFRACTION12chain 'B' and (resid 341 through 377 )
13X-RAY DIFFRACTION13chain 'B' and (resid 378 through 414 )

+
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