[English] 日本語
Yorodumi
- PDB-4ntm: QueD soaked with sepiapterin (selenomethionine substituted protein) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ntm
TitleQueD soaked with sepiapterin (selenomethionine substituted protein)
Components6-carboxy-5,6,7,8-tetrahydropterin synthase
KeywordsLYASE / T-fold / 6-PTPS / queuosine biosynthesis enzyme / sepiapterin
Function / homology
Function and homology information


6-carboxytetrahydropterin synthase / 6-carboxytetrahydropterin synthase activity / tRNA queuosine(34) biosynthetic process / zinc ion binding / identical protein binding
Similarity search - Function
6-pyruvoyl tetrahydropterin synthase/QueD / 6-pyruvoyl tetrahydropterin synthase/QueD family / 6-pyruvoyl tetrahydropterin synthase/QueD superfamily / 6-pyruvoyl tetrahydropterin synthase / Tetrahydropterin Synthase; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2K8 / 6-carboxy-5,6,7,8-tetrahydropterin synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBandarian, V. / Miles, Z.D. / Roberts, S.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Biochemical and Structural Studies of 6-Carboxy-5,6,7,8-tetrahydropterin Synthase Reveal the Molecular Basis of Catalytic Promiscuity within the Tunnel-fold Superfamily.
Authors: Miles, Z.D. / Roberts, S.A. / McCarty, R.M. / Bandarian, V.
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 6-carboxy-5,6,7,8-tetrahydropterin synthase
B: 6-carboxy-5,6,7,8-tetrahydropterin synthase
C: 6-carboxy-5,6,7,8-tetrahydropterin synthase
D: 6-carboxy-5,6,7,8-tetrahydropterin synthase
E: 6-carboxy-5,6,7,8-tetrahydropterin synthase
F: 6-carboxy-5,6,7,8-tetrahydropterin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,54218
Polymers83,8836
Non-polymers1,66012
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13960 Å2
ΔGint-118 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.297, 111.297, 126.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-339-

HOH

-
Components

#1: Protein
6-carboxy-5,6,7,8-tetrahydropterin synthase / CPH4 synthase / Queuosine biosynthesis protein QueD


Mass: 13980.462 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2765, JW2735, queD, ygcM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P65870, 6-carboxytetrahydropterin synthase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-2K8 / (6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid / 6-carboxy-5,6,7,8-tetrahydropterin


Mass: 211.178 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H9N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 4% PEG 4000, 0.1 M sodium acetate soaked 1 hour with 7mM sepiapterin 17% PEG8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→39 Å / Num. all: 63356 / Num. obs: 63356 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 23.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.01135 / Mean I/σ(I) obs: 2 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→33.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.101 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25465 2544 5.1 %RANDOM
Rwork0.2245 ---
obs0.22604 47712 99.51 %-
all-59464 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.868 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2--0.85 Å2-0 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.05→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5644 0 96 113 5853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196058
X-RAY DIFFRACTIONr_bond_other_d0.0010.025605
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9528234
X-RAY DIFFRACTIONr_angle_other_deg0.737312946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7425723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23623.053262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20515901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5421530
X-RAY DIFFRACTIONr_chiral_restr0.0720.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021422
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5151.6482877
X-RAY DIFFRACTIONr_mcbond_other0.5151.6472876
X-RAY DIFFRACTIONr_mcangle_it0.9022.4673605
X-RAY DIFFRACTIONr_mcangle_other1.6142.8263606
X-RAY DIFFRACTIONr_scbond_it1.711.8033181
X-RAY DIFFRACTIONr_scbond_other2.2532.0773180
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9043.0544630
X-RAY DIFFRACTIONr_long_range_B_refined6.22117.1716922
X-RAY DIFFRACTIONr_long_range_B_other6.2117.1026905
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 179 -
Rwork0.333 3333 -
obs--95 %
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)
14.0889-0.19811.73391.5841-0.9224.48590.0066-0.9561-0.67210.2399-0.05830.03460.535-0.03790.05170.41180.01130.08030.8120.25110.5056-33.082.14690.6474
26.0568-0.8728-0.83611.58320.87382.1707-0.1263-0.4165-0.11570.02460.00740.130.1149-0.04970.11890.0847-0.0111-0.02310.3749-0.05490.1631-30.788917.6626-19.7372
33.77661.8313-1.42983.5809-0.95241.46150.0762-1.4010.03810.2862-0.1050.09650.16970.25170.02880.40530.008-0.03081.5836-0.05850.1565-19.019620.878718.0876
43.3926-0.3220.87992.05680.27795.073-0.1-0.97070.34740.3050.001-0.0111-0.0992-0.06090.0990.09840.06250.00120.9114-0.30210.389-38.332932.37713.0024
52.47680.55060.13463.03020.07112.15820.0301-0.4025-0.36360.22530.18690.01850.34470.2835-0.2170.17450.1022-0.0380.601-0.0050.2475-8.28259.3153-8.2519
65.3346-1.0137-0.03372.43591.15711.539-0.0279-0.75420.55060.10860.0330.1306-0.08880.0308-0.00520.1441-0.06540.02070.7325-0.22990.3307-12.447836.1255-2.4878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 120
2X-RAY DIFFRACTION2B2 - 121
3X-RAY DIFFRACTION3C3 - 119
4X-RAY DIFFRACTION4D2 - 121
5X-RAY DIFFRACTION5E3 - 120
6X-RAY DIFFRACTION6F4 - 121

+
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