[English] 日本語
Yorodumi
- PDB-3hxa: Crystal Structure of DCoH1Thr51Ser -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hxa
TitleCrystal Structure of DCoH1Thr51Ser
ComponentsPterin-4-alpha-carbinolamine dehydratase
KeywordsLYASE / alpha and beta structure / Nucleus / Tetrahydrobiopterin biosynthesis
Function / homology
Function and homology information


Phenylalanine metabolism / regulation of protein binding / 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / L-phenylalanine metabolic process / phenylalanine 4-monooxygenase activity / tetrahydrobiopterin biosynthetic process / transcription coactivator activity / positive regulation of DNA-templated transcription / identical protein binding ...Phenylalanine metabolism / regulation of protein binding / 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / L-phenylalanine metabolic process / phenylalanine 4-monooxygenase activity / tetrahydrobiopterin biosynthetic process / transcription coactivator activity / positive regulation of DNA-templated transcription / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Transcriptional coactivator/pterin dehydratase / Pterin 4 alpha carbinolamine dehydratase / Pterin 4 alpha carbinolamine dehydratase superfamily / Pterin 4 alpha carbinolamine dehydratase / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pterin-4-alpha-carbinolamine dehydratase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsRho, H.Y. / Jones, C.N. / Rose, R.B.
Citation
Journal: To be Published
Title: Crystal Structure of DCoH1Thr51Ser
Authors: Rho, H.Y. / Jones, C.N. / Rose, R.B.
#1: Journal: Science / Year: 1995
Title: Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator
Authors: Endrizzi, J.A. / Cronk, J.D. / Wang, W. / Crabtree, G.R. / Alber, T.
#2: Journal: Biochemistry / Year: 2004
Title: Biochemical and structural basis for partially redundant enzymatic and transcriptional functions of DCoH and DCoH2
Authors: Rose, R.B. / Pullen, K.E. / Bayle, J.H. / Crabtree, G.R. / Alber, T.
History
DepositionJun 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pterin-4-alpha-carbinolamine dehydratase
B: Pterin-4-alpha-carbinolamine dehydratase
C: Pterin-4-alpha-carbinolamine dehydratase
D: Pterin-4-alpha-carbinolamine dehydratase
E: Pterin-4-alpha-carbinolamine dehydratase
F: Pterin-4-alpha-carbinolamine dehydratase
G: Pterin-4-alpha-carbinolamine dehydratase
H: Pterin-4-alpha-carbinolamine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,53424
Polymers96,0298
Non-polymers1,50516
Water9,440524
1
A: Pterin-4-alpha-carbinolamine dehydratase
B: Pterin-4-alpha-carbinolamine dehydratase
C: Pterin-4-alpha-carbinolamine dehydratase
D: Pterin-4-alpha-carbinolamine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,67511
Polymers48,0144
Non-polymers6617
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-100 kcal/mol
Surface area17430 Å2
MethodPISA
2
E: Pterin-4-alpha-carbinolamine dehydratase
F: Pterin-4-alpha-carbinolamine dehydratase
G: Pterin-4-alpha-carbinolamine dehydratase
H: Pterin-4-alpha-carbinolamine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,85913
Polymers48,0144
Non-polymers8459
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-104 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.805, 103.805, 193.629
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein
Pterin-4-alpha-carbinolamine dehydratase / PHS / 4-alpha-hydroxy-tetrahydropterin dehydratase / Phenylalanine hydroxylase-stimulating protein ...PHS / 4-alpha-hydroxy-tetrahydropterin dehydratase / Phenylalanine hydroxylase-stimulating protein / Pterin carbinolamine dehydratase / PCD / Dimerization cofactor of hepatocyte nuclear factor 1-alpha / Dimerization cofactor of HNF1 / DCoH


Mass: 12003.576 Da / Num. of mol.: 8 / Mutation: T51S
Source method: isolated from a genetically manipulated source
Details: GST-FUSION / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dcoh, Pcbd, PCBD/DCoH, Pcbd1 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P61459, 4a-hydroxytetrahydrobiopterin dehydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 7.5
Details: HEPES, Ammonium Sulfate, PEG 200, Glycerol, pH 7.5, Hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→81.54 Å / Num. obs: 111375 / % possible obs: 99.1 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 2.958
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.98.20.9210.8129054156950.92196.6
1.9-2.019.70.571.2146377151410.5798.7
2.01-2.159.70.3282.1138188143150.32899
2.15-2.329.70.2192.9129545134190.21999.6
2.32-2.559.80.1693.7121502124330.16999.8
2.55-2.85100.1254.3112804113100.125100
2.85-3.2910.30.1054.810259099930.105100
3.29-4.0210.60.0995.19030985230.099100
4.02-5.6910.80.0835.57255766880.083100
5.69-81.5410.40.0864.34022338580.086100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.1.9data scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.226 5521 4.9 %
Rwork0.211 --
obs-111045 98.8 %
Solvent computationBsol: 57.222 Å2
Displacement parametersBiso max: 73.94 Å2 / Biso mean: 32.07 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å2-0.342 Å20 Å2
2---2.29 Å20 Å2
3---4.581 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6305 0 88 524 6917
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.198
X-RAY DIFFRACTIONc_mcbond_it1.2261.5
X-RAY DIFFRACTIONc_scbond_it1.8762
X-RAY DIFFRACTIONc_mcangle_it1.9122
X-RAY DIFFRACTIONc_scangle_it2.8082.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5gol.paramgol.top

+
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