[English] 日本語
Yorodumi
- PDB-4pxh: Structure of P450sky (CYP163B3), a cytochrome P450 from skyllamyc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pxh
TitleStructure of P450sky (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis in complex with a peptidyl carrier protein domain
Components
  • P450 monooxygenase
  • Peptide synthetase
KeywordsOXIDOREDUCTASE/PROTEIN BINDING / Cytochrome P450 fold / beta-aminoacyl carrier protein hydroxylase / peptidyl carrier protein domains / skyllamycin NRPS / OXIDOREDUCTASE-PROTEIN BINDING complex
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / amino acid activation for nonribosomal peptide biosynthetic process / steroid hydroxylase activity / secondary metabolite biosynthetic process / cholesterol catabolic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process / iron ion binding ...cholest-4-en-3-one 26-monooxygenase activity / amino acid activation for nonribosomal peptide biosynthetic process / steroid hydroxylase activity / secondary metabolite biosynthetic process / cholesterol catabolic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / ACP-like / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. ...Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / ACP-like / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-dependent synthetase/ligase / Polyketide synthase, phosphopantetheine-binding domain / AMP-binding enzyme / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-KH4 / Peptide synthetase / p450 monooxygenase
Similarity search - Component
Biological speciesStreptomyces sp. Acta 2897 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHaslinger, K. / Cryle, M.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: The structure of a transient complex of a nonribosomal Peptide synthetase and a cytochrome p450 monooxygenase.
Authors: Haslinger, K. / Brieke, C. / Uhlmann, S. / Sieverling, L. / Sussmuth, R.D. / Cryle, M.J.
History
DepositionMar 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Sep 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_conn_type / 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.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.conn_type_id / _struct_conn.id / _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_type.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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P450 monooxygenase
B: Peptide synthetase
C: P450 monooxygenase
D: Peptide synthetase
E: P450 monooxygenase
F: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,87412
Polymers178,6676
Non-polymers3,2076
Water1,31573
1
A: P450 monooxygenase
B: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6254
Polymers59,5562
Non-polymers1,0692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-36 kcal/mol
Surface area21120 Å2
MethodPISA
2
C: P450 monooxygenase
D: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6254
Polymers59,5562
Non-polymers1,0692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-35 kcal/mol
Surface area20780 Å2
MethodPISA
3
E: P450 monooxygenase
F: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6254
Polymers59,5562
Non-polymers1,0692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-35 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.700, 161.700, 337.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein P450 monooxygenase / cytochrome P450 sky32 (CYP163B3)


Mass: 49369.414 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Acta 2897 (bacteria) / Strain: Acta 2897 / Gene: sky32 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: F2YRY7, unspecific monooxygenase
#2: Protein Peptide synthetase / PCP7


Mass: 10186.228 Da / Num. of mol.: 3 / Fragment: peptidyl carrier protein domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Acta 2897 (bacteria) / Strain: Acta 2897 / Gene: sky30 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: F2YRY5
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-KH4 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] 1H-imidazole-4-carbothioate


Mass: 452.420 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H25N4O8PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3350, 0.15 M calcium acetate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.7→47.893 Å / Num. all: 72148 / Num. obs: 72098 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 19.7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 24.5
Reflection shellResolution: 2.7→3 Å / Redundancy: 19.9 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 5.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PWV

4pwv


Resolution: 2.7→47.893 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.913 / SU B: 19.736 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24598 3577 5 %RANDOM
Rwork0.2145 ---
obs0.21608 68521 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.081 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å20 Å2
2--1.04 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11443 0 213 73 11729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211932
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.871.99916256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.31151454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95723.67575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68115.0231925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.09915107
X-RAY DIFFRACTIONr_chiral_restr0.0580.21803
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219179
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1731.57262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.333211712
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.49234670
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8424.54539
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 231 -
Rwork0.27 4981 -
obs--100 %
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)
11.2563-0.64320.81192.8953-0.37931.9209-0.07680.13750.16880.16090.0018-0.2148-0.05630.22450.07510.03560.0098-0.01420.14280.09210.0907-33.331569.978-13.7048
211.8302-5.01839.52723.9613-4.124215.76830.38231.0293-0.0003-0.1395-0.498-0.16160.61471.11560.11570.27820.1373-0.06420.4210.15320.1515-9.584559.147211.0096
31.10170.5139-0.40253.3203-0.37761.4469-0.0299-0.0286-0.1625-0.2010.0069-0.10240.12540.12860.0230.1018-0.0058-0.01870.05030.0460.0794-31.7749115.319212.2987
414.15445.5886-11.533.3256-3.844216.66270.2265-0.18610.1587-0.1261-0.15980.047-0.15980.2067-0.06670.2650.03670.07670.16650.12010.1553-7.073128.7556-9.9663
53.0877-0.40820.74511.83370.16722.4628-0.2182-0.29720.434-0.04860.06960.2481-0.2893-0.29940.14870.11830.0093-0.13850.13910.00570.23-76.6339101.129440.823
69.45815.16196.74017.02476.080215.1487-0.46120.12610.159-0.05880.39490.0856-0.3350.39370.06620.34510.024-0.21360.2698-0.08370.2835-53.673115.894664.0012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 423
2X-RAY DIFFRACTION2B6 - 80
3X-RAY DIFFRACTION3C11 - 419
4X-RAY DIFFRACTION4D6 - 79
5X-RAY DIFFRACTION5E11 - 417
6X-RAY DIFFRACTION6F6 - 79

+
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