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- PDB-5mr0: Thermophilic archaeal branched-chain amino acid transaminases fro... -

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Basic information

Entry
Database: PDB / ID: 5mr0
TitleThermophilic archaeal branched-chain amino acid transaminases from Geoglobus acetivorans and Archaeoglobus fulgidus: biochemical and structural characterisation
Components(Putative branched-chain-amino-acid ...) x 2
KeywordsTRANSFERASE / Thermophilic archaea / branch-chain transaminases / substrate specificity
Function / homology
Function and homology information


L-leucine-2-oxoglutarate transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / L-leucine biosynthetic process / L-valine biosynthetic process / isoleucine biosynthetic process
Similarity search - Function
Branched-chain amino acid aminotransferase I / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / : / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes ...Branched-chain amino acid aminotransferase I / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / : / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID / Putative branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsIsupov, M.N. / Littlechild, J.A. / James, P. / Sayer, C. / Sutter, J.M. / Schmidt, M. / Schoenheit, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L002035/1 United Kingdom
CitationJournal: Front Bioeng Biotechnol / Year: 2019
Title: Thermostable Branched-Chain Amino Acid Transaminases From the ArchaeaGeoglobus acetivoransandArchaeoglobus fulgidus: Biochemical and Structural Characterization.
Authors: Isupov, M.N. / Boyko, K.M. / Sutter, J.M. / James, P. / Sayer, C. / Schmidt, M. / Schonheit, P. / Nikolaeva, A.Y. / Stekhanova, T.N. / Mardanov, A.V. / Ravin, N.V. / Bezsudnova, E.Y. / ...Authors: Isupov, M.N. / Boyko, K.M. / Sutter, J.M. / James, P. / Sayer, C. / Schmidt, M. / Schonheit, P. / Nikolaeva, A.Y. / Stekhanova, T.N. / Mardanov, A.V. / Ravin, N.V. / Bezsudnova, E.Y. / Popov, V.O. / Littlechild, J.A.
History
DepositionDec 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative branched-chain-amino-acid aminotransferase
B: Putative branched-chain-amino-acid aminotransferase
C: Putative branched-chain-amino-acid aminotransferase
D: Putative branched-chain-amino-acid aminotransferase
E: Putative branched-chain-amino-acid aminotransferase
F: Putative branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,15032
Polymers194,6466
Non-polymers3,50426
Water13,169731
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35940 Å2
ΔGint-217 kcal/mol
Surface area53790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.210, 140.230, 168.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 290 / Label seq-ID: 1 - 290

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Putative branched-chain-amino-acid ... , 2 types, 6 molecules ABCDEF

#1: Protein
Putative branched-chain-amino-acid aminotransferase / BCAT / Transaminase B


Mass: 32403.014 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: ilvE, AF_0933 / Production host: Escherichia coli (E. coli)
References: UniProt: O29329, branched-chain-amino-acid transaminase
#2: Protein Putative branched-chain-amino-acid aminotransferase / BCAT / Transaminase B


Mass: 32631.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: ilvE, AF_0933 / Production host: Escherichia coli (E. coli)
References: UniProt: O29329, branched-chain-amino-acid transaminase

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Non-polymers , 6 types, 757 molecules

#3: Chemical
ChemComp-PXG / 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID


Mass: 368.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C15H17N2O7P
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5
Details: 0.1 M Sodium cacodylate, 0.2 M Magnesium chloride hexahydrate, 50 % v/v PEG 200, 5mM gabaculine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.98→67.13 Å / Num. obs: 119864 / % possible obs: 99 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.2
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 4.7 % / Rmerge(I) obs: 2.07 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.249 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2eiy

2eiy


Resolution: 1.98→64.72 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.512 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.20942 6000 5 %RANDOM
Rwork0.17971 ---
obs0.18122 113796 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.134 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0 Å2-0 Å2
2--0.33 Å2-0 Å2
3---0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.98→64.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13566 0 223 731 14520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01915057
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.99920558
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09551994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.03123.893732
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.168152753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.02315142
X-RAY DIFFRACTIONr_chiral_restr0.110.22291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111570
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.457.6947189
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.09214.299041
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.4769.1337868
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.89876.27963149
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A193560.07
12B193560.07
21A192760.08
22C192760.08
31A193800.07
32D193800.07
41A194140.07
42E194140.07
51A193380.08
52F193380.08
61B193060.07
62C193060.07
71B193680.07
72D193680.07
81B193240.07
82E193240.07
91B192380.08
92F192380.08
101C190280.08
102D190280.08
111C190800.07
112E190800.07
121C191140.07
122F191140.07
131D192380.08
132E192380.08
141D190380.08
142F190380.08
151E192920.07
152F192920.07
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 385 -
Rwork0.337 8139 -
obs--96.4 %

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