[English] 日本語
Yorodumi
- PDB-1nbu: 7,8-Dihydroneopterin Aldolase Complexed with Product From Mycobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nbu
Title7,8-Dihydroneopterin Aldolase Complexed with Product From Mycobacterium Tuberculosis
Components(Probable dihydroneopterin aldolase) x 3
KeywordsLYASE / anti-parallel / beta-sheet / two alpha helices / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


7,8-dihydroneopterin oxygenase / 7,8-dihydroneopterin epimerase / dihydroneopterin aldolase / dihydroneopterin aldolase activity / encapsulin nanocompartment / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / isomerase activity / oxidoreductase activity / cytoplasm
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PH2 / Dihydroneopterin aldolase / Dihydroneopterin aldolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 1.6 Å
AuthorsGoulding, C.W. / Apostol, M.I. / Sawaya, M.R. / Phillips, M. / Parseghian, A. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Regulation by oligomerization in a mycobacterial folate biosynthetic enzyme.
Authors: Goulding, C.W. / Apostol, M.I. / Sawaya, M.R. / Phillips, M. / Parseghian, A. / Eisenberg, D.
History
DepositionDec 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable dihydroneopterin aldolase
B: Probable dihydroneopterin aldolase
C: Probable dihydroneopterin aldolase
D: Probable dihydroneopterin aldolase
E: Probable dihydroneopterin aldolase
F: Probable dihydroneopterin aldolase
G: Probable dihydroneopterin aldolase
H: Probable dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,35316
Polymers105,7918
Non-polymers1,5618
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24690 Å2
ΔGint-77 kcal/mol
Surface area33420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.560, 85.150, 74.790
Angle α, β, γ (deg.)90.00, 112.69, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Probable dihydroneopterin aldolase / DHNA


Mass: 13251.920 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: FOLB OR RV3607C OR MT3712.1 OR MTCY07H7B.15 / Plasmid: pET22b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A580, UniProt: P9WNC5*PLUS, dihydroneopterin aldolase
#2: Protein Probable dihydroneopterin aldolase / DHNA


Mass: 13207.910 Da / Num. of mol.: 2 / Mutation: D19A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: FOLB OR RV3607C OR MT3712.1 OR MTCY07H7B.15 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A580, UniProt: P9WNC5*PLUS, dihydroneopterin aldolase
#3: Protein Probable dihydroneopterin aldolase / DHNA


Mass: 13115.813 Da / Num. of mol.: 1 / Mutation: Y18A, D19A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: FOLB OR RV3607C OR MT3712.1 OR MTCY07H7B.15 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A580, UniProt: P9WNC5*PLUS, dihydroneopterin aldolase
#4: Chemical
ChemComp-PH2 / 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE


Mass: 195.179 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H9N5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 1.73 Å3/Da / Density % sol: 29 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein1drop
2350 mM1dropNaCl
350 mMTris-HCl1droppH7.4
411 %PEG40001reservoir
50.1 M1reservoirLiSO4
60.1 Msodium acetate1reservoirpH4.6

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 17, 2002 / Details: mirrors
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→90 Å / Num. all: 118185 / Num. obs: 118185 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.068
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.464 / % possible all: 93.9
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 118216 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 93.9 % / Num. unique obs: 111905 / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 1DHN

1dhn


Resolution: 1.6→10 Å / Num. parameters: 71829 / Num. restraintsaints: 90056 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF), Author states ARG23 of chain A, ARG23 of chain B, ARG15 of chain C, ARG15 of chain E, ARG23 of chain E and ARG23 of chain F all have two distinct conformations.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4817 -RANDOM
Rwork0.166 ---
all0.177 111758 --
obs0.177 109918 93.8 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7947.25
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7406 0 112 470 7988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0263
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps0.07
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.2

+
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://pdbjlvh1.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