[English] 日本語
Yorodumi
- PDB-8vmk: A crystal structure of heme-dependent tyrosine hydroxylase comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vmk
TitleA crystal structure of heme-dependent tyrosine hydroxylase complexed with a substrate analog, 3-(4-hydroxyphenyl)propionic acid
ComponentsHeme-dependent L-tyrosine hydroxylase
KeywordsOXIDOREDUCTASE/INHIBITOR / tyrosine hydroxylase / heme enzyme / binary complex / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / HYDROXYPHENYL PROPIONIC ACID
Function and homology information
Biological speciesStreptomyces sclerotialus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsWang, Y. / Traore, E. / 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: To Be Published
Title: A crystal structure of heme-dependent tyrosine hydroxylase complexed with a substrate analog, 3-(4-hydroxyphenyl)propionic acid
Authors: Traore, E. / Wang, Y. / Liu, A.
History
DepositionJan 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

-
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)71,0568
Polymers69,2462
Non-polymers1,8106
Water10,449580
1
A: Heme-dependent L-tyrosine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5284
Polymers34,6231
Non-polymers9053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme-dependent L-tyrosine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5284
Polymers34,6231
Non-polymers9053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.634, 129.819, 48.420
Angle α, β, γ (deg.)90.00, 93.86, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#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 BL21(DE3) (bacteria)
#2: Chemical ChemComp-HPP / HYDROXYPHENYL PROPIONIC ACID


Mass: 166.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 %
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: APS / Beamline: 19-BM / Wavelength: 0.96682 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96682 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 82562 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.56-1.594.30.49140660.8090.9460.2590.5580.47798.9
1.59-1.624.90.43441140.8720.9650.2120.4850.513100
1.62-1.6550.37641610.8990.9730.1850.420.546100
1.65-1.6850.32641400.9250.980.1590.3640.577100
1.68-1.7250.27741300.9420.9850.1340.3080.616100
1.72-1.7650.25441700.9530.9880.1230.2830.665100
1.76-1.850.22141360.9570.9890.1070.2460.722100
1.8-1.8550.18741400.9690.9920.0910.2090.79799.9
1.85-1.950.16641410.9730.9930.080.1850.903100
1.9-1.9750.14641420.9780.9950.0710.1631.02399.9
1.97-2.0450.12941300.9820.9950.0620.1431.17699.9
2.04-2.1250.11441520.9850.9960.0550.1271.24299.7
2.12-2.214.90.09741240.9870.9970.0480.1091.26399.7
2.21-2.334.90.08941500.990.9970.0440.11.30799.5
2.33-2.484.90.08441220.990.9970.0420.0941.36199.4
2.48-2.674.80.08441210.9870.9970.0420.0941.52799.1
2.67-2.944.80.08641290.9870.9970.0430.0961.91799.1
2.94-3.364.80.07940900.990.9980.040.0892.03498.2
3.36-4.234.50.05540820.9920.9980.030.0631.41897.7
4.23-504.70.04941220.9950.9990.0250.0561.24997.3

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→48.31 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 1977 2.4 %
Rwork0.1869 --
obs0.1875 82515 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4681 0 126 580 5387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074978
X-RAY DIFFRACTIONf_angle_d0.9846820
X-RAY DIFFRACTIONf_dihedral_angle_d9.968712
X-RAY DIFFRACTIONf_chiral_restr0.052725
X-RAY DIFFRACTIONf_plane_restr0.01890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.27421220.23525650X-RAY DIFFRACTION98
1.6-1.640.21471450.2155763X-RAY DIFFRACTION100
1.64-1.690.29141530.22295751X-RAY DIFFRACTION100
1.69-1.750.25531400.21035754X-RAY DIFFRACTION100
1.75-1.810.22691340.19925842X-RAY DIFFRACTION100
1.81-1.880.21031640.19835727X-RAY DIFFRACTION100
1.88-1.970.23191210.20035815X-RAY DIFFRACTION100
1.97-2.070.2361420.19495791X-RAY DIFFRACTION100
2.07-2.20.22811400.18965800X-RAY DIFFRACTION100
2.2-2.370.22191430.18835729X-RAY DIFFRACTION99
2.37-2.610.22181450.19065750X-RAY DIFFRACTION99
2.61-2.980.22051410.19695772X-RAY DIFFRACTION99
2.98-3.760.18941380.17315692X-RAY DIFFRACTION98
3.76-48.310.19011490.16855702X-RAY DIFFRACTION97

+
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