[English] 日本語
Yorodumi
- PDB-3oa3: Crystal structure of a putative deoxyribose-phosphate aldolase fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oa3
TitleCrystal structure of a putative deoxyribose-phosphate aldolase from Coccidioides immitis
Componentsaldolase
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / putative uncharacterized protein / aldolase / Coccidioides / pathogenic fungus / coccidioidomycosis / Valley Fever / meningitis / agriculture
Function / homology
Function and homology information


deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / carbohydrate catabolic process / cytoplasm
Similarity search - Function
Deoxyribose-phosphate aldolase type I / Deoxyribose-phosphate aldolase / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of an unknown aldolase from Coccidioides immitis
Authors: Edwards, T.E. / Gardberg, A.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: aldolase
B: aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4934
Polymers62,3752
Non-polymers1182
Water9,134507
1
A: aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2462
Polymers31,1871
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2462
Polymers31,1871
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: aldolase
hetero molecules

B: aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4934
Polymers62,3752
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area1270 Å2
ΔGint-6 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.690, 80.810, 71.670
Angle α, β, γ (deg.)90.000, 102.990, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein aldolase


Mass: 31187.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (fungus) / Production host: Escherichia coli (E. coli)
References: UniProt: E0CX06*PLUS, deoxyribose-phosphate aldolase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 4.93 mg/mL CoimA.00559.a.A1 PS00460 against Hampton Index Screen condition G9, 0.2 M ammonium sulphate, 0.1 M Tris pH 8.5, 25% PEG 3350 enheanced with 20% glycerol as cryo-protectant, ...Details: 4.93 mg/mL CoimA.00559.a.A1 PS00460 against Hampton Index Screen condition G9, 0.2 M ammonium sulphate, 0.1 M Tris pH 8.5, 25% PEG 3350 enheanced with 20% glycerol as cryo-protectant, crystal tracking ID 216774g9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 69876 / Num. obs: 68464 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 23.315 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.41
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.640.385425368498096.5
1.64-1.690.3294.724800485796.7
1.69-1.740.2785.424078470996.9
1.74-1.790.2286.723582461397.1
1.79-1.850.188822932447697.2
1.85-1.910.14610.322310436397.7
1.91-1.980.11812.721060418497.7
1.98-2.070.08616.620512404498
2.07-2.160.07519.319362387798.1
2.16-2.260.05923.418928375098.5
2.26-2.390.05425.717517355998.3
2.39-2.530.04927.916839335798.7
2.53-2.70.04430.815824317298.9
2.7-2.920.0433.814599296499.3
2.92-3.20.03637.113511274599
3.2-3.580.03439.911739248199.7
3.58-4.130.0342.910287218699.1
4.13-5.060.02645.59367186999.7
5.06-7.160.02644.57337146299.8
7.160.02246.8399181699.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.64 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å46.47 Å
Translation3 Å46.47 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGJ molecule A

3ngj


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1915 / WRfactor Rwork: 0.1621 / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.9013 / SU B: 2.844 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0817 / SU Rfree: 0.0831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 3443 5 %RANDOM
Rwork0.163 ---
obs0.1646 68409 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.66 Å2 / Biso mean: 21.0965 Å2 / Biso min: 9.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-0.22 Å2
2--0.06 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 8 507 4267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224000
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9715486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61524.805154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9615698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.731523
X-RAY DIFFRACTIONr_chiral_restr0.0820.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212987
X-RAY DIFFRACTIONr_mcbond_it0.5461.52615
X-RAY DIFFRACTIONr_mcangle_it1.01424242
X-RAY DIFFRACTIONr_scbond_it1.731385
X-RAY DIFFRACTIONr_scangle_it2.9254.51208
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 236 -
Rwork0.202 4738 -
all-4974 -
obs--96.47 %
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)
10.3048-0.0692-0.03040.29650.17540.1046-0.023-0.0409-0.0224-0.01850.01610.0191-0.01160.0120.00690.03230.00360.00280.02480.00760.032837.856137.38751.7349
20.2543-0.14660.15880.0893-0.12760.58980.00650.0522-0.02940.0023-0.02090.0195-0.01630.06580.01440.02110.0046-0.00730.04570.01740.024121.921738.2043-30.5816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

+
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