[English] 日本語
Yorodumi
- PDB-5hdm: Crystal structure of Arabidopsis thaliana glutamate-1-semialdehyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hdm
TitleCrystal structure of Arabidopsis thaliana glutamate-1-semialdehyde-2,1-aminomutase
ComponentsGlutamate-1-semialdehyde 2,1-aminomutase 1, chloroplastic
KeywordsISOMERASE / Arabidopsis thaliana / glutamate-1-semialdehyde-2 / 1-aminomutase / PMP / PLP
Function / homology
Function and homology information


glutamate-1-semialdehyde 2,1-aminomutase / glutamate-1-semialdehyde 2,1-aminomutase activity / chlorophyll biosynthetic process / porphyrin-containing compound biosynthetic process / apoplast / protoporphyrinogen IX biosynthetic process / chloroplast envelope / plastid / chloroplast stroma / transaminase activity ...glutamate-1-semialdehyde 2,1-aminomutase / glutamate-1-semialdehyde 2,1-aminomutase activity / chlorophyll biosynthetic process / porphyrin-containing compound biosynthetic process / apoplast / protoporphyrinogen IX biosynthetic process / chloroplast envelope / plastid / chloroplast stroma / transaminase activity / chloroplast / pyridoxal phosphate binding / protein homodimerization activity / cytosol
Similarity search - Function
Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 ...Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Glutamate-1-semialdehyde 2,1-aminomutase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSong, Y. / Pu, H. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Fundation of China31471267 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from Arabidopsis thaliana.
Authors: Song, Y. / Pu, H. / Jiang, T. / Zhang, L. / Ouyang, M.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate-1-semialdehyde 2,1-aminomutase 1, chloroplastic
B: Glutamate-1-semialdehyde 2,1-aminomutase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5575
Polymers92,8142
Non-polymers7433
Water19,6541091
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
ΔGint-50 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.117, 109.331, 115.502
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glutamate-1-semialdehyde 2,1-aminomutase 1, chloroplastic / / AtGSA1 / GSA 1 / Glutamate-1-semialdehyde aminotransferase 1 / GSA-AT 1


Mass: 46406.969 Da / Num. of mol.: 2 / Fragment: UNP residues 41-474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GSA1, HEML1, At5g63570, MBK5.3 / Production host: Escherichia coli (E. coli)
References: UniProt: P42799, glutamate-1-semialdehyde 2,1-aminomutase
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1091 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: potassium bromide, PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 212729 / % possible obs: 95 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.48 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.026 / Rrim(I) all: 0.057 / Χ2: 0.924 / Net I/av σ(I): 22.062 / Net I/σ(I): 11 / Num. measured all: 829276
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.25-1.293.70.32213000.9160.1810.370.92396
1.29-1.353.70.253212900.9430.1430.2920.94396
1.35-1.413.70.197214050.9640.1110.2280.95696.3
1.41-1.483.80.152214120.9760.0840.1750.96196.4
1.48-1.573.80.109215370.9870.060.1250.96996.6
1.57-1.73.80.079214880.9920.0430.0910.88496.4
1.7-1.873.90.062214530.9950.0320.070.86495.9
1.87-2.1440.058213650.9950.030.0661.16495.2
2.14-2.694.10.052211050.9960.0260.0581.13793.5
2.69-504.40.031203740.9980.0160.0350.48587.8

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155: ???refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
ARPmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSA

2gsa


Resolution: 1.25→28.875 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1498 10210 4.99 %
Rwork0.1264 194420 -
obs0.1275 204630 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.98 Å2 / Biso mean: 18.4883 Å2 / Biso min: 4.36 Å2
Refinement stepCycle: final / Resolution: 1.25→28.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6422 0 47 1091 7560
Biso mean--17.84 33.67 -
Num. residues----856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076944
X-RAY DIFFRACTIONf_angle_d1.0919466
X-RAY DIFFRACTIONf_chiral_restr0.0841037
X-RAY DIFFRACTIONf_plane_restr0.0081242
X-RAY DIFFRACTIONf_dihedral_angle_d13.6242614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2495-1.26370.20772510.16494601485266
1.2637-1.27860.18172940.14765152544673
1.2786-1.29420.19172720.14585515578778
1.2942-1.31060.19873220.14495806612883
1.3106-1.32780.17423130.13566048636186
1.3278-1.3460.17313450.13246260660589
1.346-1.36530.16543240.13146498682292
1.3653-1.38560.17023380.12686541687993
1.3856-1.40730.15513210.1276706702795
1.4073-1.43040.15223580.12386759711796
1.4304-1.4550.16883320.12146825715796
1.455-1.48150.16173280.12056814714297
1.4815-1.510.14993990.11396717711697
1.51-1.54080.15093670.10646848721596
1.5408-1.57430.15033710.10616806717797
1.5743-1.61090.14783460.10266801714796
1.6109-1.65120.15923570.10456863722097
1.6512-1.69580.15063600.10446785714596
1.6958-1.74570.14243840.1096772715696
1.7457-1.80210.14273440.11026799714396
1.8021-1.86650.14953500.11376805715596
1.8665-1.94120.14413550.1136781713696
1.9412-2.02950.15643440.11716788713295
2.0295-2.13650.14653580.11746741709995
2.1365-2.27030.14243220.11896756707894
2.2703-2.44550.14383630.12566673703694
2.4455-2.69140.1443900.13246598698893
2.6914-3.08050.14763400.1396572691291
3.0805-3.87960.13153170.12756607692491
3.8796-28.88320.16123450.15086183652882

+
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