[English] 日本語
Yorodumi
- PDB-4f4e: Crystal structure of Aromatic-amino-acid aminotransferase from Bu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f4e
TitleCrystal structure of Aromatic-amino-acid aminotransferase from Burkholderia pseudomallei covalently bound to pyridoxal phosphate
ComponentsAromatic-amino-acid aminotransferase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / pyridoxal phosphate lysine
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding
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
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Aromatic-amino-acid aminotransferase from Burkholderia pseudomallei covalently bound to pyridoxal phosphate
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Clifton, M.C. / Staker, B.L. / Myler, P. / Stewart, L.J.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Sep 13, 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_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 / _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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aromatic-amino-acid aminotransferase
B: Aromatic-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0996
Polymers90,8512
Non-polymers2484
Water15,475859
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-15 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.920, 74.820, 85.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Aromatic-amino-acid aminotransferase


Mass: 45425.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: BPSS0355, tyrB / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q63NE4, aromatic-amino-acid transaminase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Emerald Bio JCSG+ screen C1: 20% PEG8000, 100 mM phosphate/citrate, pH 4.2, 200 mM sodium chloride, 36.1 mg/mL BupsE.01471.a.A1 PW 34948 + 2.5 mM PLP, tray 233390c1, cryoprotectant: 10/20% ...Details: Emerald Bio JCSG+ screen C1: 20% PEG8000, 100 mM phosphate/citrate, pH 4.2, 200 mM sodium chloride, 36.1 mg/mL BupsE.01471.a.A1 PW 34948 + 2.5 mM PLP, tray 233390c1, cryoprotectant: 10/20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 9, 2012
RadiationMonochromator: RIGAKU VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 80697 / Num. obs: 80481 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 22.744 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.8530.4652.4717069578198.7
1.85-1.93.10.4052.8517587574599.4
1.9-1.953.20.3143.7717672556299.6
1.95-2.013.30.2564.817847540599.8
2.01-2.083.40.2135.9318151529199.8
2.08-2.153.90.1728.0819775507799.8
2.15-2.234.60.14210.9822587492499.9
2.23-2.324.80.12313.0422856475499.9
2.32-2.4350.10715.222911455699.9
2.43-2.555.30.09617.3823241436099.9
2.55-2.685.70.08220.37238374152100
2.68-2.856.60.07324.55261423974100
2.85-3.047.30.0630.52271443704100
3.04-3.297.30.04836.8254533478100
3.29-3.67.30.03846.35235033213100
3.6-4.027.30.0359.07212492915100
4.02-4.657.20.02764.3188042598100
4.65-5.697.20.02759.03160162224100
5.69-8.057.10.02856.9123281747100
8.05-506.40.01781.556486102198

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.8 Å36.05 Å
Translation1.8 Å36.05 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EFF

4eff


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.1683 / WRfactor Rwork: 0.1382 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8971 / SU B: 4.159 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1114 / SU Rfree: 0.1086 / Isotropic thermal model: ISOTROPIC, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 4037 5 %RANDOM
Rwork0.1607 ---
all0.1625 80697 --
obs0.1625 80427 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.1 Å2 / Biso mean: 17.3325 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5996 0 16 859 6871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196213
X-RAY DIFFRACTIONr_bond_other_d0.0010.024119
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.978474
X-RAY DIFFRACTIONr_angle_other_deg0.963310006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7723.209268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87915950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9861556
X-RAY DIFFRACTIONr_chiral_restr0.0930.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021316
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 264 -
Rwork0.246 5196 -
all-5460 -
obs-5781 98.5 %
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)
10.3930.21340.14630.41450.0850.43860.0602-0.058-0.0510.0194-0.0527-0.05360.03120.0182-0.00740.0166-0.0082-0.00180.02990.02110.0207115.04914.78969.946
20.5867-0.04910.37660.39590.0160.5699-0.0229-0.06350.0077-0.0077-0.01990.0925-0.0722-0.11150.04280.01110.0148-0.00820.0229-0.0110.032986.60120.80949.791
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 399
2X-RAY DIFFRACTION1A500 - 501
3X-RAY DIFFRACTION2B1 - 399
4X-RAY DIFFRACTION2B500 - 501

+
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