[English] 日本語
Yorodumi
- PDB-2dhn: COMPLEX OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AURE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dhn
TitleCOMPLEX OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AUREUS WITH 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 2.2 A RESOLUTION
Components7,8-DIHYDRONEOPTERIN ALDOLASE
KeywordsPRODUCT COMPLEX / PTERINE BINDING / FOLATE BIOSYNTHESIS / ANTIBIOTIC TARGET / BETA-BARREL
Function / homology
Function and homology information


7,8-dihydroneopterin epimerase / dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / isomerase activity / tetrahydrofolate biosynthetic process / 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
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.2 Å
AuthorsHennig, M. / D'Arcy, A. / Hampele, I.C. / Page, M.G.P. / Oefner, C.H. / Dale, G.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure and reaction mechanism of 7,8-dihydroneopterin aldolase from Staphylococcus aureus.
Authors: Hennig, M. / D'Arcy, A. / Hampele, I.C. / Page, M.G. / Oefner, C. / Dale, G.E.
History
DepositionMar 31, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 7,8-DIHYDRONEOPTERIN ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,7701
Non-polymers1951
Water1,33374
1
A: 7,8-DIHYDRONEOPTERIN ALDOLASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)111,71916
Polymers110,1578
Non-polymers1,5618
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area26350 Å2
ΔGint-80 kcal/mol
Surface area34030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.200, 62.200, 123.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein 7,8-DIHYDRONEOPTERIN ALDOLASE / DHNA


Mass: 13769.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: DHNA / Plasmid: PSADHNA / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (PREP4) / References: UniProt: P56740
#2: Chemical ChemComp-PH2 / 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE


Mass: 195.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.143.41
2
Crystal growpH: 6.6 / Details: pH 6.6
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1200 mMmagnesium formate1drop
2175 mMmagnesium formate1reservoir

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 1997 / Details: MIRROR
RadiationMonochromator: SUPPER MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 27653 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.9 / % possible all: 98.6
Reflection
*PLUS
Num. obs: 6008 / Num. measured all: 27653

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: molecular replacement
Starting model: DHNA UNLIGANDED

Resolution: 2.2→30 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: RFREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.298 -5 %RANDOM
Rwork0.202 ---
obs0.202 6008 95.9 %-
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 14 74 1055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.86
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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