[English] 日本語
Yorodumi
- PDB-2v6u: High resolution crystal structure of pterin-4a-carbinolamine dehy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v6u
TitleHigh resolution crystal structure of pterin-4a-carbinolamine dehydratase from Toxoplasma gondii
ComponentsPTERIN-4A-CARBINOLAMINE DEHYDRATASE
KeywordsLYASE / PTERIN / ENZYME / TOXOPLASMA / DEHYDRATASE
Function / homology
Function and homology information


4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / tetrahydrobiopterin biosynthetic process
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
4a-hydroxytetrahydrobiopterin dehydratase
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsCameron, S. / Goldie, S.P. / Hunter, W.N.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2008
Title: Crystal Structures of Toxoplasma Gondii Pterin-4A-Carbinolamine Dehydratase and Comparisons with Mammalian and Parasite Orthologues.
Authors: Cameron, S. / Fyffe, S.A. / Goldie, S.P. / Hunter, W.N.
History
DepositionJul 20, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
B: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9303
Polymers23,9072
Non-polymers231
Water5,170287
1
A: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
B: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
hetero molecules

A: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
B: PTERIN-4A-CARBINOLAMINE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8606
Polymers47,8144
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area7810 Å2
ΔGint-43.1 kcal/mol
Surface area22890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)120.135, 120.135, 49.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.013, 0.954, -0.3), (0.959, -0.074, -0.275), (-0.284, -0.292, -0.913)
Vector: 0.56138, 0.52293, -0.47242)

-
Components

#1: Protein PTERIN-4A-CARBINOLAMINE DEHYDRATASE


Mass: 11953.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Plasmid: MODIFIED PET15B (NOVAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2Q449, 4a-hydroxytetrahydrobiopterin dehydratase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 3.22 Å3/Da / Density % sol: 64.5 %
Description: PDB ENTRY 2V6S WAS USED AS A STARTING POINT FOR RIGID BODY REFINEMENT
Crystal growpH: 7.6
Details: 1.4 M AMMONIUM SULPHATE, 1 M LITHIUM SULPHATE, pH 7.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0064
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 17, 2006 / Details: MIRROR
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 1.6→53.8 Å / Num. obs: 47707 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.8 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2V6S

2v6s


Resolution: 1.6→53.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.981 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2420 5.1 %RANDOM
Rwork0.172 ---
obs0.173 45288 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→53.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 1 287 1930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9481.8992401
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8385210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62823.95896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58415295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.818158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021374
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.2778
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21191
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4491.51027
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86321648
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4833778
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.374.5742
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 165
Rwork0.219 3255
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.3002-3.5962-1.58174.72040.7691.72330.0446-0.22140.11620.3014-0.0665-0.1322-0.0120.0320.0218-0.0211-0.0174-0.04560.0222-0.00190.0072-7.53843.1175.44
21.42210.63740.99640.86640.31541.20190.01780.0287-0.05370.004-0.0003-0.08230.020.0395-0.0175-0.0163-0.0096-0.0007-0.0022-0.0090.0347-17.13637.188-9.215
33.26842.76323.18654.66923.84886.5670.1490.0089-0.29060.27750.0467-0.26760.33740.1261-0.1957-0.0183-0.0236-0.0445-0.00250.00690.0684-16.26430.566-5.046
41.20520.8022-1.11041.4554-1.48452.6772-0.03360.10860.147-0.01510.10330.1853-0.1261-0.1531-0.06970.01350.00620.003-0.02590.03510.0574-30.12353.045-28.385
51.52880.64520.02431.91660.39352.86340.0050.00450.0976-0.01940.07350.0807-0.0151-0.0383-0.0784-0.003-0.00180.0032-0.02870.02020.0272-30.40940.519-16.74
62.0381.8237-1.80871.9699-1.60755.2647-0.01320.18080.0171-0.12570.13220.09420.0747-0.2763-0.1190.0135-0.0004-0.0035-0.02840.04950.0427-32.09645.409-26.195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 85
3X-RAY DIFFRACTION3A86 - 103
4X-RAY DIFFRACTION4B5 - 40
5X-RAY DIFFRACTION5B41 - 73
6X-RAY DIFFRACTION6B74 - 103

+
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