[English] 日本語
Yorodumi
- PDB-3h14: Crystal structure of a putative aminotransferase from Silicibacte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h14
TitleCrystal structure of a putative aminotransferase from Silicibacter pomeroyi
ComponentsAminotransferase, classes I and II
KeywordsTRANSFERASE / Aminotransferase / Silicibacter pomeroyi / YP_167802.1 / SPO2589 / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / Pyridoxal phosphate / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
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 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSampathkumar, P. / Atwell, S. / Wasserman, S. / Miller, S. / Bain, K. / Rutter, M. / Tarun, G. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative aminotransferase from Silicibacter pomeroyi
Authors: Sampathkumar, P.
History
DepositionApr 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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: Aminotransferase, classes I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8813
Polymers42,6961
Non-polymers1842
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aminotransferase, classes I and II
hetero molecules

A: Aminotransferase, classes I and II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7616
Polymers85,3932
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4260 Å2
ΔGint-24.1 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.367, 86.376, 144.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Aminotransferase, classes I and II


Mass: 42696.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Strain: DSS-3 / DSM 15171 / Gene: SPO2589, YP_167802.1 / Plasmid: BC-pSGX3(BC), modified pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: Q5LQA4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 200mM Calcium acetate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 9, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.9→21.81 Å / Num. obs: 29683 / % possible obs: 99.9 % / Redundancy: 14.6 % / Biso Wilson estimate: 19.559 Å2 / Rsym value: 0.098 / Net I/σ(I): 17
Reflection shellResolution: 1.9→2 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 4287 / Rsym value: 0.489 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→21.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.627 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.15
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1503 5.1 %RANDOM
Rwork0.189 ---
obs0.192 29645 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.17 Å2 / Biso mean: 25.844 Å2 / Biso min: 14.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 12 231 2970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222822
X-RAY DIFFRACTIONr_bond_other_d0.0020.021865
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9753850
X-RAY DIFFRACTIONr_angle_other_deg0.97134534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4455377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75223.248117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02215412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6631523
X-RAY DIFFRACTIONr_chiral_restr0.0860.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02584
X-RAY DIFFRACTIONr_nbd_refined0.2180.2557
X-RAY DIFFRACTIONr_nbd_other0.1940.22038
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21431
X-RAY DIFFRACTIONr_nbtor_other0.0880.21458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.29
X-RAY DIFFRACTIONr_mcbond_it1.1651.52010
X-RAY DIFFRACTIONr_mcbond_other0.2511.5754
X-RAY DIFFRACTIONr_mcangle_it1.36922941
X-RAY DIFFRACTIONr_scbond_it2.69431051
X-RAY DIFFRACTIONr_scangle_it3.574.5904
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 117 -
Rwork0.249 2044 -
all-2161 -
obs-2044 100 %

+
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