[English] 日本語
Yorodumi
- PDB-2nm2: Crystal structure of dihydroneopterin aldolase from S. aureus in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nm2
TitleCrystal structure of dihydroneopterin aldolase from S. aureus in complex with (1S,2R)-neopterin at 1.50 Angstrom resolution
ComponentsDihydroneopterin aldolase
KeywordsLYASE / DIHYDRONEOPTERIN ALDOLASE / DHNA / SUBSTRATE COMPLEX / MONAPTERIN / NEOPTERIN / 7 / 8-DIHYDRONEOPTERIN / DRUG DESIGN
Function / homology
Function and homology information


7,8-dihydroneopterin epimerase / dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / isomerase 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
L-NEOPTERIN / Dihydroneopterin aldolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBlaszczyk, J. / Ji, X. / Yan, H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural basis for the aldolase and epimerase activities of Staphylococcus aureus dihydroneopterin aldolase.
Authors: Blaszczyk, J. / Li, Y. / Gan, J. / Yan, H. / Ji, X.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_initial_refinement_model
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydroneopterin aldolase
B: Dihydroneopterin aldolase
C: Dihydroneopterin aldolase
D: Dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0918
Polymers55,0794
Non-polymers1,0134
Water11,566642
1
A: Dihydroneopterin aldolase
B: Dihydroneopterin aldolase
C: Dihydroneopterin aldolase
D: Dihydroneopterin aldolase
hetero molecules

A: Dihydroneopterin aldolase
B: Dihydroneopterin aldolase
C: Dihydroneopterin aldolase
D: Dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,18316
Polymers110,1578
Non-polymers2,0268
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area26100 Å2
ΔGint-112 kcal/mol
Surface area34750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.033, 60.033, 123.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11A-1322-

HOH

21A-1406-

HOH

31A-1636-

HOH

41B-1481-

HOH

51B-1577-

HOH

61C-1600-

HOH

-
Components

#1: Protein
Dihydroneopterin aldolase / DHNA


Mass: 13769.635 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folB / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / Strain (production host): PLYSS / References: UniProt: P56740, dihydroneopterin aldolase
#2: Chemical
ChemComp-NEU / L-NEOPTERIN / 2-AMINO-6-((1S,2R)-1,2,3-TRIHYDROXYPROPYL)PTERIDIN-4(3H)-ONE


Mass: 253.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / 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: 2.01 Å3/Da / Density % sol: 38.9 %
Description: CRYSTALS WERE MEROHEDRALLY TWINNED WITH PERFECT (50%) TWINNING RATIO
Crystal growTemperature: 292 K / pH: 7.5
Details: 0.8M Sodium-potassium tartrate, 0.1M HEPES, 10mM Tris-HCL, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97148
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 5, 2003 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97148 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 43915 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 1.98 / % possible all: 88.3

-
Processing

Software
NameVersionClassification
CNS1refinement
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NM3

2nm3


Resolution: 1.7→22.46 Å / Rfactor Rfree error: 0.008 / Num. parameters: 16296 / Num. restraintsaints: 16509 / Data cutoff high absF: 69025.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: CRYSTAL IS TWINED. TWIN OPERATOR H, -K TWIN FRACTION 0.50.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2047 4.3 %RANDOM
Rwork0.22 ---
obs0.22 42055 88 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.61 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4685
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-30 Å
Luzzati sigma a0.6 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 1.7→22.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 72 642 4582
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.642
X-RAY DIFFRACTIONc_scangle_it3.952.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.337 253 4.3 %
Rwork0.334 4420 -
obs--78.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION5NEU.PARNEU.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://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