[English] 日本語
Yorodumi
- PDB-20zq: Crystal structure of rice HPPD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 20zq
TitleCrystal structure of rice HPPD
Components4-hydroxyphenylpyruvate dioxygenase
KeywordsOXIDOREDUCTASE / hydroxyphenylpyruvate dioxygenase / rice
Function / homology
Function and homology information


4-hydroxyphenylpyruvate dioxygenase activity / L-tyrosine catabolic process / L-phenylalanine catabolic process / metal ion binding / cytoplasm
Similarity search - Function
4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase, C-terminal / 4-hydroxyphenylpyruvate dioxygenase, N-terminal / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 4-hydroxyphenylpyruvate dioxygenase
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, L. / Ran, T. / Wang, W.W. / Zhang, B.L.
Funding support China, 3items
OrganizationGrant numberCountry
Jiangsu Key Research and Development ProgramBE2022365 China
the Basic Research Program of JiangsuBK20241182 China
Zhongshan Biological Breeding LaboratoryZSBBL-KY2023-04 China
CitationJournal: To Be Published
Title: structure of rice hydroxyphenylpyruvate dioxygenase
Authors: Chen, L. / Ran, T.T. / Wang, W.W. / Zhang, B.L.
History
DepositionDec 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxyphenylpyruvate dioxygenase
B: 4-hydroxyphenylpyruvate dioxygenase
C: 4-hydroxyphenylpyruvate dioxygenase
D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,39014
Polymers192,2424
Non-polymers1,14910
Water14,664814
1
A: 4-hydroxyphenylpyruvate dioxygenase
D: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,13910
Polymers96,1212
Non-polymers1,0188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-22 kcal/mol
Surface area30450 Å2
MethodPISA
2
B: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules

C: 4-hydroxyphenylpyruvate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2524
Polymers96,1212
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3700 Å2
ΔGint-24 kcal/mol
Surface area31020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.064, 93.436, 113.957
Angle α, β, γ (deg.)90.00, 109.85, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
4-hydroxyphenylpyruvate dioxygenase


Mass: 48060.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Oryza sativa is not available at the time of biocuration. Current sequence reference is from UniProt ID A0A0E0G1W2.
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E0G1W2

-
Non-polymers , 5 types, 824 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 814 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 293 K / Method: evaporation / Details: PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 127948 / % possible obs: 98.2 % / Redundancy: 3.4 % / CC1/2: 0.988 / Rpim(I) all: 0.126 / Net I/σ(I): 3.4
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 6325 / CC1/2: 0.508 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 6219 4.87 %
Rwork0.1989 --
obs0.201 127785 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12361 0 63 818 13242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812769
X-RAY DIFFRACTIONf_angle_d0.9817294
X-RAY DIFFRACTIONf_dihedral_angle_d6.9841818
X-RAY DIFFRACTIONf_chiral_restr0.0591838
X-RAY DIFFRACTIONf_plane_restr0.0122347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.38462060.34674018X-RAY DIFFRACTION98
1.92-1.940.3631730.3144097X-RAY DIFFRACTION98
1.94-1.970.3122020.30794035X-RAY DIFFRACTION98
1.97-1.990.34031970.29634084X-RAY DIFFRACTION98
1.99-2.020.31912110.28754010X-RAY DIFFRACTION98
2.02-2.050.332050.28093979X-RAY DIFFRACTION97
2.05-2.080.3132000.26694009X-RAY DIFFRACTION97
2.08-2.110.30422150.25324055X-RAY DIFFRACTION99
2.11-2.140.28122270.23834015X-RAY DIFFRACTION99
2.14-2.170.28872040.22374062X-RAY DIFFRACTION99
2.17-2.210.27312200.21364089X-RAY DIFFRACTION99
2.21-2.250.2831760.21994042X-RAY DIFFRACTION98
2.25-2.30.2832030.21424071X-RAY DIFFRACTION98
2.3-2.340.24972340.20374055X-RAY DIFFRACTION98
2.34-2.390.23722080.1954042X-RAY DIFFRACTION98
2.39-2.450.24612140.20433998X-RAY DIFFRACTION98
2.45-2.510.27981970.2043974X-RAY DIFFRACTION95
2.51-2.580.27042130.19854043X-RAY DIFFRACTION99
2.58-2.650.26222300.18934059X-RAY DIFFRACTION98
2.65-2.740.22732210.18714060X-RAY DIFFRACTION99
2.74-2.840.24612060.18274086X-RAY DIFFRACTION99
2.84-2.950.26791760.1914136X-RAY DIFFRACTION99
2.95-3.080.24342130.19394066X-RAY DIFFRACTION98
3.08-3.250.25662190.1933964X-RAY DIFFRACTION96
3.25-3.450.19142710.18154030X-RAY DIFFRACTION99
3.45-3.710.22012140.1744092X-RAY DIFFRACTION99
3.71-4.080.19812010.16314102X-RAY DIFFRACTION98
4.08-4.670.18641680.1484104X-RAY DIFFRACTION97
4.67-5.860.18582150.16254058X-RAY DIFFRACTION98
5.86-100.18161800.16754131X-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