[English] 日本語
Yorodumi
- PDB-3r2e: Dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r2e
TitleDihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase from Yersinia pestis.
ComponentsDihydroneopterin aldolase
KeywordsLYASE / structural genomics / IDP90567 / Center for Structural Genomics of Infectious Diseases / CSGID / bifunctional / dihydroneopterin aldolase / dihydroneopterin triphosphate 2'-epimerase
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid-containing compound metabolic process / folic acid biosynthetic process / 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
7,8-dihydroneopterin aldolase / 7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsOsipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase from Yersinia pestis
Authors: Osipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydroneopterin aldolase


Theoretical massNumber of molelcules
Total (without water)16,1491
Polymers16,1491
Non-polymers00
Water19811
1
A: Dihydroneopterin aldolase
x 8


Theoretical massNumber of molelcules
Total (without water)129,1938
Polymers129,1938
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area17530 Å2
ΔGint-82 kcal/mol
Surface area40290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.716, 71.716, 107.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Dihydroneopterin aldolase


Mass: 16149.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO-92 / Gene: folB, YPO0648 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0WJ22, UniProt: A0A5P8YJX5*PLUS, dihydroneopterin aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M calcium chloride, 0.1 M Bis-tris buffer, 45% MPD, 10 mM guanine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 24, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→31 Å / Num. all: 7990 / Num. obs: 7990 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.595 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.15-2.195.80.8552.053951.183100
2.19-2.236.20.7033871.192100
2.23-2.2770.8273921.208100
2.27-2.3270.6924051.311100
2.32-2.377.20.5793721.375100
2.37-2.4270.5664031.279100
2.42-2.4870.4653881.407100
2.48-2.557.10.3673971.359100
2.55-2.6270.3083901.51100
2.62-2.7170.2273911.511100
2.71-2.817.10.1884011.549100
2.81-2.9270.1713921.624100
2.92-3.0570.1213971.90299.7
3.05-3.216.90.0894041.835100
3.21-3.416.90.0684012.01399.8
3.41-3.686.90.0554032.05499.8
3.68-4.056.80.0444081.997100
4.05-4.636.70.0374142.01998.6
4.63-5.836.70.0324071.6699
5.83-505.90.0324431.79495.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O90

2o90


Resolution: 2.15→31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 16.998 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 368 4.6 %RANDOM
Rwork0.2153 ---
all0.2171 7960 --
obs0.2171 7960 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 157.66 Å2 / Biso mean: 67.9161 Å2 / Biso min: 33.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.15→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 0 11 933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022943
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9371279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8815118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24824.89447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.88915167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.711157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02711
X-RAY DIFFRACTIONr_mcbond_it0.9271.5582
X-RAY DIFFRACTIONr_mcangle_it1.7232942
X-RAY DIFFRACTIONr_scbond_it2.6483361
X-RAY DIFFRACTIONr_scangle_it4.4454.5336
LS refinement shellResolution: 2.15→2.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 27 -
Rwork0.298 540 -
all-567 -
obs-567 98.61 %
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)
19.6459-2.6312-7.51486.96144.069211.2237-0.0337-0.80360.31040.19950.2334-0.418-0.17690.6606-0.19960.4312-0.0477-0.1380.4247-0.04430.339711.507413.102912.9308
26.749-1.3949-2.09745.90030.53686.91680.0649-0.55560.7890.4735-0.0484-0.5696-0.5480.5993-0.01640.2696-0.0984-0.11520.2822-0.20430.34316.654716.813115.0975
33.4716-1.9178-0.222214.10557.88516.1364-0.3046-0.61170.30550.00360.0914-0.0198-0.11710.35830.21330.2652-0.0262-0.14110.3899-0.03270.264212.85016.856116.5528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 47
2X-RAY DIFFRACTION2A48 - 85
3X-RAY DIFFRACTION3A86 - 116

+
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