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- PDB-6xwb: Crystal structure of an R-selective transaminase from Thermomyces... -

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Basic information

Entry
Database: PDB / ID: 6xwb
TitleCrystal structure of an R-selective transaminase from Thermomyces stellatus.
ComponentsR-selective transaminase
KeywordsTRANSFERASE / transaminase
Function / homologyAminotransferase 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta / PYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesThermomyces stellatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGourlay, L.J.
CitationJournal: Front Bioeng Biotechnol / Year: 2020
Title: An ( R )-Selective Transaminase From Thermomyces stellatus : Stabilizing the Tetrameric Form.
Authors: Heckmann, C.M. / Gourlay, L.J. / Dominguez, B. / Paradisi, F.
History
DepositionJan 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 1.2Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R-selective transaminase
B: R-selective transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,93227
Polymers81,0892
Non-polymers1,84425
Water2,972165
1
A: R-selective transaminase
hetero molecules

A: R-selective transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,28934
Polymers81,0892
Non-polymers2,20032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10010 Å2
ΔGint10 kcal/mol
Surface area24730 Å2
MethodPISA
2
B: R-selective transaminase
hetero molecules

B: R-selective transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,57620
Polymers81,0892
Non-polymers1,48718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8430 Å2
ΔGint17 kcal/mol
Surface area25320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.770, 98.010, 117.258
Angle α, β, γ (deg.)90.000, 91.218, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 1 through 319 or resid 501 through 1301))A1 - 319
121(chain 'A' and (resid 1 through 319 or resid 501 through 1301))A501
131(chain 'A' and (resid 1 through 319 or resid 501 through 1301))A601
141(chain 'A' and (resid 1 through 319 or resid 501 through 1301))A701
151(chain 'A' and (resid 1 through 319 or resid 501 through 1301))A801
161(chain 'A' and (resid 1 through 319 or resid 501 through 1301))A1001
171(chain 'A' and (resid 1 through 319 or resid 501 through 1301))A1101
181(chain 'A' and (resid 1 through 319 or resid 501 through 1301))A1201
191(chain 'A' and (resid 1 through 319 or resid 501 through 1301))A1301
2101(chain 'B' and (resid 1 through 34 or (resid 35...B1 - 319
2111(chain 'B' and (resid 1 through 34 or (resid 35...B601
2121(chain 'B' and (resid 1 through 34 or (resid 35...B701
2131(chain 'B' and (resid 1 through 34 or (resid 35...B901
2141(chain 'B' and (resid 1 through 34 or (resid 35...B1001
2151(chain 'B' and (resid 1 through 34 or (resid 35...B1101
2161(chain 'B' and (resid 1 through 34 or (resid 35...B1201
2171(chain 'B' and (resid 1 through 34 or (resid 35...B1401
2181(chain 'B' and (resid 1 through 34 or (resid 35...B1501

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Components

#1: Protein R-selective transaminase


Mass: 40544.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein terminates at residue Q355 / Source: (gene. exp.) Thermomyces stellatus (fungus) / Gene: Thest2p7_019146 / Production host: Escherichia coli (E. coli)
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Microseeding with microcrystals grown in PACT condition G3. Larger crystals grew in seeded drops in PACT condition D12.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→59 Å / Num. obs: 38936 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 23.82 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.075 / Rrim(I) all: 0.135 / Χ2: 0.79 / Net I/σ(I): 10.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 20731 / CC1/2: 0.912 / Rpim(I) all: 0.347 / Rrim(I) all: 0.632 / Χ2: 0.75 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ce5

4ce5


Resolution: 2.2→37.6 Å / SU ML: 0.2419 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.3615
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2307 1998 5.14 %
Rwork0.2007 36889 -
obs0.2023 38887 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 0 116 165 5259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565189
X-RAY DIFFRACTIONf_angle_d0.7237004
X-RAY DIFFRACTIONf_chiral_restr0.0524756
X-RAY DIFFRACTIONf_plane_restr0.005902
X-RAY DIFFRACTIONf_dihedral_angle_d15.28533077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.25911420.2282652X-RAY DIFFRACTION99.96
2.26-2.320.27061400.23872579X-RAY DIFFRACTION99.71
2.32-2.380.26171440.21642651X-RAY DIFFRACTION99.86
2.38-2.460.28821420.2182603X-RAY DIFFRACTION99.82
2.46-2.550.24871350.22482620X-RAY DIFFRACTION99.93
2.55-2.650.24281510.20852613X-RAY DIFFRACTION99.78
2.65-2.770.25551430.20552641X-RAY DIFFRACTION99.93
2.77-2.920.25911350.20592632X-RAY DIFFRACTION99.89
2.92-3.10.21641440.20062651X-RAY DIFFRACTION99.96
3.1-3.340.24551450.20962613X-RAY DIFFRACTION99.96
3.34-3.680.20361410.19272649X-RAY DIFFRACTION99.93
3.68-4.210.21211480.17562644X-RAY DIFFRACTION99.75
4.21-5.30.1831420.16692652X-RAY DIFFRACTION99.96
5.3-37.60.24161460.21882689X-RAY DIFFRACTION99.75

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