[English] 日本語
Yorodumi
- PDB-3meb: Structure of cytoplasmic aspartate aminotransferase from giardia ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3meb
TitleStructure of cytoplasmic aspartate aminotransferase from giardia lamblia
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / ASPARTATE AMINOTRANSFERASE / Aminotransferase / Pyridoxal phosphate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / amino acid metabolic process / biosynthetic process / pyridoxal phosphate binding / mitochondrion
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structures of aspartate aminotransferases from Trypanosoma brucei, Leishmania major and Giardia lamblia.
Authors: Abendroth, J. / Choi, R. / Wall, A. / Clifton, M.C. / Lukacs, C.M. / Staker, B.L. / Van Voorhis, W. / Myler, P. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2May 6, 2015Group: Database references
Revision 1.3May 13, 2015Group: Database references
Revision 1.4May 27, 2015Group: Database references
Revision 1.5Sep 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_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspartate aminotransferase
B: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,69222
Polymers99,9452
Non-polymers1,74720
Water14,574809
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.580, 101.150, 81.530
Angle α, β, γ (deg.)90.00, 90.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 6 / Auth seq-ID: 1 - 425 / Label seq-ID: 22 - 446

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Aspartate aminotransferase


Mass: 49972.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / Gene: GL50803_91056 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8B1V5, aspartate transaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.54 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: HR INDEX SCREEN G3: 20% PEG 3350, 200MM LI2 SULPHATE, 100MM BISTRISPROPANE, GILAA.01471.A AT 35 MG/ML, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 15, 2010 / Details: Rigaku VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 74816 / Num. obs: 71707 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 19.09 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.85
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3 / Num. unique all: 5548 / % possible all: 87.3

-
Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2cst modified with CCP4 program CHAINSAW

2cst


Resolution: 1.9→47.81 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.971 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3613 5 %RANDOM
Rwork0.174 ---
all0.176 74816 --
obs0.176 71615 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-0.25 Å2
2--1.54 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6612 0 108 809 7529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226923
X-RAY DIFFRACTIONr_bond_other_d0.0010.024665
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9579367
X-RAY DIFFRACTIONr_angle_other_deg0.931311363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66923.798287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6961524
X-RAY DIFFRACTIONr_chiral_restr0.0870.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021441
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5981.54257
X-RAY DIFFRACTIONr_mcbond_other0.1691.51731
X-RAY DIFFRACTIONr_mcangle_it1.05426820
X-RAY DIFFRACTIONr_scbond_it1.79432666
X-RAY DIFFRACTIONr_scangle_it2.7734.52542
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5563 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.275
Bloose thermal0.8410
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 218 -
Rwork0.227 4613 -
obs--87.17 %
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)
10.2992-0.0732-0.03880.14470.04510.57690.00910.0378-0.03240.00290.0009-0.01760.0822-0.0076-0.010.0903-0.00340.03620.0278-0.00250.04391.02638.70218.996
20.3595-0.06410.00790.41290.16711.4622-0.01440.0780.0594-0.04650.0130.0398-0.1430.04890.00140.0952-0.01170.02790.04940.01510.05736.95756.9297.574
30.67360.1550.04950.34030.02940.3813-0.01330.0627-0.0036-0.00610.0187-0.02550.0580.0734-0.00540.08110.01010.02970.04840.00040.037413.36343.30818.442
40.6963-0.1568-0.06521.0102-0.4362.24840.05790.09170.0048-0.11820.00820.03540.0576-0.2449-0.06610.0908-0.00960.01020.08060.00140.0091-12.26341.462-3.89
50.3363-0.0463-0.030.0981-0.0510.79030.0258-0.0142-0.04520.0352-0.01160.00390.15480.0301-0.01410.10990.01130.030.01390.00310.05050.25938.29436.161
60.308-0.0013-0.21120.6093-0.04391.07620.0137-0.02770.0170.07320.0001-0.021-0.08190.0207-0.01380.1-0.00070.02420.0274-0.00750.0563-5.72957.07547.495
70.4546-0.14540.07870.302-0.09090.346-0.0091-0.0431-0.00490.01140.01670.02090.0577-0.0808-0.00760.0879-0.01190.03430.0373-0.00340.049-11.88143.32336.445
80.76460.13580.04191.08730.30782.9270.0636-0.1015-0.05210.0982-0.0123-0.08010.11080.354-0.05130.07130.02490.01090.11360.00870.017213.51841.56758.709
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2A104 - 232
3X-RAY DIFFRACTION3A233 - 329
4X-RAY DIFFRACTION4A330 - 425
5X-RAY DIFFRACTION5B1 - 103
6X-RAY DIFFRACTION6B104 - 231
7X-RAY DIFFRACTION7B232 - 329
8X-RAY DIFFRACTION8B330 - 426

+
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