[English] 日本語
Yorodumi
- PDB-4ffc: Crystal structure of a 4-aminobutyrate aminotransferase (GabT) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ffc
TitleCrystal structure of a 4-aminobutyrate aminotransferase (GabT) from Mycobacterium abscessus
Components4-aminobutyrate aminotransferase (GabT)
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / GabT / pyridoxal phosphate binding / aminotransferase
Function / homology
Function and homology information


4-aminobutyrate transaminase activity / gamma-aminobutyric acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
4-aminobutyrate aminotransferase, bacterial / 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 ...4-aminobutyrate aminotransferase, bacterial / 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
4-aminobutyrate aminotransferase (GabT)
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMay 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Sep 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 1.4Dec 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: 4-aminobutyrate aminotransferase (GabT)
B: 4-aminobutyrate aminotransferase (GabT)
C: 4-aminobutyrate aminotransferase (GabT)
D: 4-aminobutyrate aminotransferase (GabT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,4538
Polymers188,2054
Non-polymers2484
Water34,4451912
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22740 Å2
ΔGint-96 kcal/mol
Surface area48980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.400, 67.530, 102.460
Angle α, β, γ (deg.)78.060, 81.260, 77.440
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
4-aminobutyrate aminotransferase (GabT)


Mass: 47051.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_4207 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MIQ9
#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.: 1912 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MyabA.01026.b.A1 PS00899 at 20 mg/mL against PACT F6 0.2 M sodium formate, 0.1 M Bis Tris Propane pH 6.5, 20% PEG 3350, crystal tracking ID 233334f6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
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 / Details: VariMax
RadiationProtocol: 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: 158993 / Num. obs: 152966 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 19.198 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 29.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.1238.03348381008085.9
1.85-1.90.1148.72356401015388.4
1.9-1.950.09510.43360371015291
1.95-2.010.08712.52364641014493.5
2.01-2.080.0714.71366441003895.9
2.08-2.150.06417.6839196992697.8
2.15-2.230.05822.2545339971298.6
2.23-2.320.06323.8442783927398.1
2.32-2.430.0527.1145846891599
2.43-2.550.05129.143138849098.7
2.55-2.680.04532.0548373823199.5
2.68-2.850.04237.9350847771299.4
2.85-3.040.03943.3554707727499.8
3.04-3.290.03647.7948080674399.6
3.29-3.60.03155.17469526273100
3.6-4.020.02861.5542425566199.9
4.02-4.650.02665.1837110496499.9
4.65-5.690.02563.55320924225100
5.69-8.050.02562.2424541324099.9
8.050.02270.7712733176098.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å41.81 Å
Translation3 Å41.81 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3oks

3oks


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1597 / WRfactor Rwork: 0.1345 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9226 / SU B: 3.447 / SU ML: 0.058 / SU R Cruickshank DPI: 0.1076 / SU Rfree: 0.0995 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1669 7697 5 %RANDOM
Rwork0.1381 ---
obs0.1396 145353 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.9 Å2 / Biso mean: 12.6276 Å2 / Biso min: 2.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0.39 Å20.2 Å2
2---0.02 Å2-0.09 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12901 0 16 1912 14829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913385
X-RAY DIFFRACTIONr_bond_other_d0.0010.028820
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9818299
X-RAY DIFFRACTIONr_angle_other_deg0.931321545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71551834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14523.097507
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.066151989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.09615113
X-RAY DIFFRACTIONr_chiral_restr0.0780.22161
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022678
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 502 -
Rwork0.164 9563 -
all-10065 -
obs--85.92 %
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)
10.11020.0094-0.02330.0589-0.02570.1505-0.00330.0304-0.02930.01410.0027-0.01160.02470.00650.00060.01110.002700.0283-0.01750.030525.6993-13.735812.3364
20.1149-0.00050.0590.05830.03590.152-0.01220.01570.01540.00590.00160.0005-0.0281-0.01570.01060.00850.0038-0.0010.033-0.00230.02016.546911.215612.3815
30.02470.0122-0.02420.1507-0.01180.14950.01340.01020.00210.0571-0.0075-0.04690.04720.0003-0.00580.05890.003-0.01820.00760.00510.016226.2202-13.492459.3873
40.0343-0.01620.05050.14650.08270.215800.00350.01130.0325-0.03090.01030.0065-0.04530.03090.0231-0.00840.01070.0293-0.01060.01156.183110.862159.4353
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 446
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION1A601 - 1088
4X-RAY DIFFRACTION2B4 - 446
5X-RAY DIFFRACTION2B501 - 997
6X-RAY DIFFRACTION3C4 - 447
7X-RAY DIFFRACTION3C501 - 502
8X-RAY DIFFRACTION3C601 - 1041
9X-RAY DIFFRACTION4D4 - 446
10X-RAY DIFFRACTION4D501 - 986

+
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