[English] 日本語
Yorodumi
- PDB-2amx: Crystal structure of Plasmodium Yoelii Adenosine deaminase (PY02076) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2amx
TitleCrystal structure of Plasmodium Yoelii Adenosine deaminase (PY02076)
Componentsadenosine deaminase
KeywordsHYDROLASE / Plasmodium Yoelii Adenosine deaminase (PY02076) / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


deaminase activity / purine ribonucleoside monophosphate biosynthetic process
Similarity search - Function
Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Adenosine deaminase domain / Adenosine deaminase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Adenosine deaminase
Similarity search - Component
Biological speciesPlasmodium yoelii (eukaryote)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.02 Å
AuthorsDong, A. / Vedadi, M. / Wasney, G. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. ...Dong, A. / Vedadi, M. / Wasney, G. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionAug 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 This entry contains the crystallographic asymmetric unit which consists of 2 chain(s) ...BIOMOLECULE: 1 This entry contains the crystallographic asymmetric unit which consists of 2 chain(s). The biological unit for the protein is not known.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: adenosine deaminase
B: adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,96713
Polymers86,6732
Non-polymers29511
Water8,917495
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.719, 90.332, 137.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein adenosine deaminase


Mass: 43336.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii (eukaryote) / Plasmid: p28-LIC-Thrombin derived from pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7RMV2, adenosine deaminase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 300 K / pH: 5.5
Details: 20% PEG 3350, 0.1 M Na cacodylate pH 5.5, 0.2 M MgCl2, 10 mM CoCl2, VAPOR DIFFUSION, temperature 300 K, pH 5.50

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 14, 2005 / Details: VERIMAX
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2SINGLE WAVELENGTHMx-ray1
1SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→42.9 Å / Num. all: 55108 / Num. obs: 55046 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 7.2
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.13 / Rsym value: 0.699 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.02→42.9 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.046 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 773 1.4 %RANDOM
Rwork0.196 ---
obs0.197 54132 99.7 %-
all-54132 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.02→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5866 0 11 495 6372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9528087
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5495717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06324.505293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.304151107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9441526
X-RAY DIFFRACTIONr_chiral_restr0.1110.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024474
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22975
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24067
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2459
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3620.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3260.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3270.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0381.53698
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69725785
X-RAY DIFFRACTIONr_scbond_it2.57932625
X-RAY DIFFRACTIONr_scangle_it3.8394.52302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 63 -
Rwork0.231 3921 -
obs--99.38 %

+
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