[English] 日本語
Yorodumi
- PDB-7kqt: A 1.84-A resolution crystal structure of heme-dependent L-tyrosin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kqt
TitleA 1.84-A resolution crystal structure of heme-dependent L-tyrosine hydroxylase in complex with 3-fluoro-L-tyrosine and cyanide
ComponentsHeme-dependent L-tyrosine hydroxylase
KeywordsOXIDOREDUCTASE / heme-binding enzyme / L-tyrosine hydroxylase
Function / homologyCYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / 3-FLUOROTYROSINE
Function and homology information
Biological speciesStreptomyces sclerotialus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.835 Å
AuthorsWang, Y. / Liu, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Molecular Rationale for Partitioning between C-H and C-F Bond Activation in Heme-Dependent Tyrosine Hydroxylase.
Authors: Wang, Y. / Davis, I. / Shin, I. / Xu, H. / Liu, A.
History
DepositionNov 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heme-dependent L-tyrosine hydroxylase
B: Heme-dependent L-tyrosine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0529
Polymers69,2462
Non-polymers1,8067
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-54 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.375, 129.446, 48.401
Angle α, β, γ (deg.)90.000, 94.290, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Heme-dependent L-tyrosine hydroxylase


Mass: 34623.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sclerotialus (bacteria) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 5 types, 311 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-YOF / 3-FLUOROTYROSINE


Type: L-peptide linking / Mass: 199.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10FNO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris (pH 6.1), 0.2 M MgCl2, and 16% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.835→50 Å / Num. obs: 49481 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.87 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.056 / Rrim(I) all: 0.146 / Χ2: 0.981 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.84-1.876.40.94824720.8270.4071.0340.4799.4
1.87-1.916.50.91725140.7990.3880.9970.59799.1
1.91-1.946.50.78524410.8180.3330.8550.80399.1
1.94-1.986.60.63525000.8950.2670.690.58899
1.98-2.036.60.52224640.9250.2190.5670.55499
2.03-2.076.50.52324730.9110.2250.5710.79698.5
2.07-2.126.50.40524500.9220.1740.4420.7498.1
2.12-2.186.10.32123520.9610.1390.3510.70693.9
2.18-2.256.60.30724390.9590.1310.3350.83797.8
2.25-2.326.80.28725010.9590.120.3111.05499.5
2.32-2.46.80.23525060.9720.0990.2550.9599.5
2.4-2.56.80.20924910.9810.0870.2270.97499.4
2.5-2.616.80.1924690.9820.0790.2061.00399.3
2.61-2.756.60.17524700.9820.0740.191.21598.4
2.75-2.926.50.14824140.9840.0630.1611.16696.1
2.92-3.157.10.13725120.9870.0560.1481.29799.5
3.15-3.466.90.12325100.9860.0510.1331.45599.6
3.46-3.966.70.10724940.990.0450.1171.59698.8
3.96-4.996.80.09224650.9920.0380.0991.49298.1
4.99-506.90.08325440.9950.0330.0891.15299.1

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.10.1refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KQR

7kqr


Resolution: 1.835→48.266 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 2003 4.06 %
Rwork0.2029 47384 -
obs0.2048 49387 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.81 Å2 / Biso mean: 43.039 Å2 / Biso min: 15.84 Å2
Refinement stepCycle: final / Resolution: 1.835→48.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 154 304 5130
Biso mean--42.39 48.98 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074971
X-RAY DIFFRACTIONf_angle_d0.8836800
X-RAY DIFFRACTIONf_chiral_restr0.048723
X-RAY DIFFRACTIONf_plane_restr0.006884
X-RAY DIFFRACTIONf_dihedral_angle_d19.0072901
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.835-1.88090.41211390.3729290285
1.8809-1.93170.41111210.3281346699
1.9317-1.98860.3271500.2874341899
1.9886-2.05280.33421590.2625341199
2.0528-2.12610.30911250.2474341298
2.1261-2.21130.26781490.2191324894
2.2113-2.31190.25381300.2057346899
2.3119-2.43380.26591590.2021342999
2.4338-2.58630.26331390.2016345499
2.5863-2.78590.27611440.205339697
2.7859-3.06620.26381430.2043340598
3.0662-3.50980.23821490.18613452100
3.5098-4.42150.18061420.1652343198
4.4215-48.2660.22461540.1862349299
Refinement TLS params.Method: refined / Origin x: 18.5993 Å / Origin y: 1.3537 Å / Origin z: 13.1792 Å
111213212223313233
T0.1452 Å20.0029 Å2-0.0109 Å2-0.2156 Å2-0.0249 Å2--0.1946 Å2
L0.4565 °2-0.1804 °2-0.17 °2-1.8455 °2-0.5122 °2--1.4878 °2
S0.0397 Å °0.0075 Å °0.017 Å °-0.1782 Å °-0.0432 Å °-0.0024 Å °-0.1055 Å °-0.0859 Å °-0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 403
2X-RAY DIFFRACTION1allB6 - 403
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 315

+
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