[English] 日本語
Yorodumi
- PDB-6zup: Psychrophilic aromatic amino acids aminotransferase from Psychrob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zup
TitlePsychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6 cocrystalized with substrate analog - L-(-)-3-phenyllactic acid
ComponentsAminotransferaseTransaminase
KeywordsTRANSFERASE / psychrophilic / aminotranasferase / cold-adapted / enzyme / complex / phenyllactic acid / inhibitor
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / identical protein binding / metal ion binding / cytosol
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID / NITRATE ION / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase
Similarity search - Component
Biological speciesPsychrobacter sp. B6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsBujacz, A. / Rum, J. / Rutkiewicz, M. / Pietrzyk-Brzezinska, A.J. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2016/21/B/ST5/00555 Poland
Citation
Journal: Materials (Basel) / Year: 2021
Title: Structural Evidence of Active Site Adaptability towards Different Sized Substrates of Aromatic Amino Acid Aminotransferase from Psychrobacter Sp. B6.
Authors: Bujacz, A. / Rum, J. / Rutkiewicz, M. / Pietrzyk-Brzezinska, A.J. / Bujacz, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6.
Authors: Bujacz, A. / Rutkiewicz-Krotewicz, M. / Nowakowska-Sapota, K. / Turkiewicz, M.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Aminotransferase
A: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,49711
Polymers88,3982
Non-polymers1,0999
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-54 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.390, 60.390, 81.940
Angle α, β, γ (deg.)90.000, 103.000, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Aminotransferase / Transaminase


Mass: 44199.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter sp. B6 (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: C7E5X4, Transferases; Transferring nitrogenous groups; Transaminases

-
Non-polymers , 5 types, 88 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-HFA / ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID


Type: L-peptide linking / Mass: 166.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M MgNO3, 20% PEG 2000, HEPES pH 7.5.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2017 / Details: Mirrors
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.49→79.84 Å / Num. obs: 23715 / % possible obs: 98.8 % / Redundancy: 3.35 % / Biso Wilson estimate: 65.53 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.123 / Χ2: 0.965 / Net I/σ(I): 8.29 / Num. measured all: 79436
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.643.2211.3560.8611992387137230.4181.62696.2
2.64-2.833.3070.8081.4611855359735850.6830.96799.7
2.83-3.053.5670.4992.5411926335733430.8530.58799.6
3.05-3.343.5110.2854.2810932312531140.9440.33699.6
3.34-3.733.3290.1467.69282280327880.9830.17599.5
3.73-4.313.1740.07413.77863249624770.9930.08999.2
4.31-5.263.4940.0520.527316211420940.9960.05999.1
5.26-7.43.1910.04322.045230166916390.9970.05298.2
7.4-79.843.1930.0333.8630409719520.9980.03698

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.9-1692refinement
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RKC

4rkc


Resolution: 2.5→79.84 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 38.538 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 967 4.1 %RANDOM
Rwork0.1989 ---
obs0.2007 22687 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.3 Å2 / Biso mean: 70.45 Å2 / Biso min: 39.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å2-0 Å20.11 Å2
2--1.19 Å20 Å2
3---1.24 Å2
Refinement stepCycle: final / Resolution: 2.5→79.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 72 79 6353
Biso mean--80.43 64.38 -
Num. residues----796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196414
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.928677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17624.384292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.543151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3061536
X-RAY DIFFRACTIONr_chiral_restr0.0960.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214902
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 78 -
Rwork0.388 1653 -
all-1731 -
obs--99.71 %
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)
11.92470.32020.18740.73310.42380.2682-0.0496-0.110.2345-0.19340.01910.0771-0.08650.06930.03050.1719-0.02330.07010.2978-0.05350.222536.501611.950614.0697
21.56820.1390.22360.08250.08160.91370.0238-0.7583-0.2645-0.10030.0025-0.029-0.04980.0554-0.02630.1576-0.04250.01310.65360.09370.2343.8317-2.240331.5528
31.24420.4698-0.12161.20420.31480.52810.0136-0.23560.1066-0.04680.1014-0.1572-0.07290.2191-0.1150.0598-0.03420.03450.3507-0.14930.272752.955417.361320.0852
41.05970.7307-0.14580.5482-0.0690.0517-0.0316-0.1092-0.2675-0.1048-0.0873-0.1454-0.03690.01470.11880.1979-0.0680.02970.3429-0.00280.317826.3056-12.414211.1907
51.15210.0389-0.49950.78910.08580.43570.0193-0.20650.0389-0.0884-0.03020.0043-0.0469-0.08380.01080.07320.01120.00820.4163-0.01740.22910.60832.657320.7832
60.73930.5237-0.51792.0105-0.00650.5171-0.06880.13110.0224-0.0642-0.01410.15630.1327-0.14160.08290.1522-0.0698-0.00290.3377-0.01090.19839.2839-17.6517.0134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 66
2X-RAY DIFFRACTION2A67 - 287
3X-RAY DIFFRACTION3A288 - 398
4X-RAY DIFFRACTION4B1 - 66
5X-RAY DIFFRACTION5B67 - 287
6X-RAY DIFFRACTION6B288 - 398

+
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