[English] 日本語
Yorodumi
- PDB-5d40: Crystal structure of the 5-selective H176Y mutant of Cytochrome TxtE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d40
TitleCrystal structure of the 5-selective H176Y mutant of Cytochrome TxtE
ComponentsP450-like protein
KeywordsOXIDOREDUCTASE / cytochrome / p450 / heme / regioselectivity / F/G loop
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
4-nitrotryptophan synthase / 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 / TRYPTOPHAN / Putative P450-like protein
Similarity search - Component
Biological speciesStreptomyces scabies (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsCahn, J.K.B. / Dodani, S.C. / Arnold, F.H.
Funding support United States, 2items
OrganizationGrant numberCountry
Gordon and Betty MooreGBMF2809 United States
US Army Research OfficeW911NF-09-0001 United States
CitationJournal: Nat.Chem. / Year: 2016
Title: Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models.
Authors: Dodani, S.C. / Kiss, G. / Cahn, J.K. / Su, Y. / Pande, V.S. / Arnold, F.H.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P450-like protein
B: P450-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,82716
Polymers94,3212
Non-polymers2,50614
Water20,8071155
1
A: P450-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1655
Polymers47,1601
Non-polymers1,0054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P450-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,66111
Polymers47,1601
Non-polymers1,50110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.721, 99.207, 105.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein P450-like protein


Mass: 47160.496 Da / Num. of mol.: 2 / Mutation: H176Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabies (strain 87.22) (bacteria)
Strain: 87.22 / Gene: SCAB_31831 / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: C9ZDC6

-
Non-polymers , 5 types, 1169 molecules

#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-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1155 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 200mM MgCl2, 100mM Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2015
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.15→72.206 Å / Num. all: 120407 / Num. obs: 120407 / % possible obs: 97.5 % / Redundancy: 4.7 % / Rpim(I) all: 0.052 / Rrim(I) all: 0.113 / Rsym value: 0.1 / Net I/av σ(I): 5.349 / Net I/σ(I): 8 / Num. measured all: 564788
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
1.51-1.5940.6011.160558152510.3380.6012.285.4
1.59-1.694.80.4291.781582168260.2180.4293.299.8
1.69-1.84.60.3182.372936157640.1650.3184.199.1
1.8-1.954.90.2083.472893148330.1060.2085.999.8
1.95-2.134.70.1374.763498135960.0710.1377.999.4
2.13-2.384.90.16.460901123930.0510.110.599.8
2.38-2.754.70.0787.951962109720.040.07812.399.6
2.75-3.3750.0598.94658793170.030.05915.799.8
3.37-4.774.70.0499.93445373000.0250.0491999.6
4.77-38.4694.70.044101941841550.0220.04417.799.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.99 Å38.47 Å
Translation5.99 Å38.47 Å

-
Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHASER2.5.6phasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TPN

4tpn


Resolution: 1.51→72.206 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2062 / WRfactor Rwork: 0.1384 / FOM work R set: 0.765 / SU B: 3.777 / SU ML: 0.061 / SU R Cruickshank DPI: 0.0952 / SU Rfree: 0.0864 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 6063 5 %RANDOM
Rwork0.1492 ---
obs0.1525 114245 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.42 Å2 / Biso mean: 13.754 Å2 / Biso min: 3.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.76 Å2
Refinement stepCycle: final / Resolution: 1.51→72.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6284 0 171 1155 7610
Biso mean--12.2 30.89 -
Num. residues----806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196696
X-RAY DIFFRACTIONr_bond_other_d0.0010.026371
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.9819180
X-RAY DIFFRACTIONr_angle_other_deg0.931314592
X-RAY DIFFRACTIONr_chiral_restr0.1450.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217653
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021599
X-RAY DIFFRACTIONr_mcbond_it1.7941.0073254
X-RAY DIFFRACTIONr_mcbond_other1.7941.0073253
X-RAY DIFFRACTIONr_mcangle_it2.1331.5174067
X-RAY DIFFRACTIONr_rigid_bond_restr3.929313067
X-RAY DIFFRACTIONr_sphericity_free34.0515386
X-RAY DIFFRACTIONr_sphericity_bonded9.656513657
LS refinement shellResolution: 1.508→1.547 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 288 -
Rwork0.262 6265 -
all-6553 -
obs--72.68 %

+
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