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- PDB-4chi: (R)-selective amine transaminase from Aspergillus fumigatus at 1.... -

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Basic information

Entry
Database: PDB / ID: 4chi
Title(R)-selective amine transaminase from Aspergillus fumigatus at 1.27 A resolution
ComponentsBRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


carboxylic acid biosynthetic process / Transferases; Transferring nitrogenous groups; Transaminases / carboxylic acid metabolic process / transaminase activity
Similarity search - Function
: / 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 ...: / 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
: / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Branched-chain amino acid aminotransferase, putative
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.27 Å
AuthorsThomsen, M. / Palm, G.J. / Hinrichs, W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystallographic Characterization of the (R)-Selective Amine Transaminase from Aspergillus Fumigatus.
Authors: Thomsen, M. / Skalden, L. / Palm, G.J. / Hohne, M. / Bornscheuer, U.T. / Hinrichs, W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the (R)-Selective Amine Transaminase from Aspergillus Fumigatus
Authors: Thomsen, M. / Skalden, L. / Palm, G.J. / Hoehne, M. / Bornscheuer, U.T. / Hinrichs, W.
History
DepositionDec 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_source
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
B: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,59718
Polymers74,3852
Non-polymers1,21316
Water18,5731031
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-110.4 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.367, 120.935, 135.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.864, -0.007, -0.504), (-0.008, -1), (-0.504, 0.004, -0.864)
Vector: 24.3019, 71.63666, 88.77213)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE / R-SELECTIVE AMINE TRANSAMINASE


Mass: 37192.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Strain: AF293 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4WH08, Transferases; Transferring nitrogenous groups; Transaminases, beta-alanine-pyruvate transaminase

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Non-polymers , 7 types, 1047 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1031 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN
Nonpolymer detailsPYRIDOXAL-5'-PHOSPHATE (PLP): COVALENTLY LINKED TO LYS179

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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: 2.9 Å3/Da / Density % sol: 58 %
Description: THE DATA SET AT WAVELENGTH 0.9184 A WAS USED FOR DATA COLLECTION STATISTICS AND REFINEMENT. THE DATA SET AT WAVELENGTH 1.7712 A WAS USED FOR S-SAD AND ANOMALOUS MAP CALCULATION.
Crystal growpH: 7.5 / Details: 20 MM TRICINE PH 7.5, 0.01 MM PLP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841,1.7712
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2013 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
21.77121
ReflectionResolution: 1.27→50 Å / Num. obs: 426722 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.38 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2
Reflection shellResolution: 1.27→1.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.27→47.88 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.972 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. OCCUPANCIES OF ANOMALOUS SCATTERERS WERE SET TO ACCOMMODATE NORMAL AND ANOMALOUS MAPS, OCCASIONALLY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. OCCUPANCIES OF ANOMALOUS SCATTERERS WERE SET TO ACCOMMODATE NORMAL AND ANOMALOUS MAPS, OCCASIONALLY RESULTING IN UNINTERPRETABLE B-FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.12697 10991 5 %RANDOM
Rwork0.10329 ---
obs0.10447 208810 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.118 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---0.24 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.27→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5043 0 62 1031 6136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196264
X-RAY DIFFRACTIONr_bond_other_d0.0010.026012
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9868717
X-RAY DIFFRACTIONr_angle_other_deg1.195314018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.785892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31723.883291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.792151107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4321546
X-RAY DIFFRACTIONr_chiral_restr0.1360.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217357
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021449
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_it2.8251.2492951
X-RAY DIFFRACTIONr_mcbond_other2.7791.2462950
X-RAY DIFFRACTIONr_mcangle_it3.1771.8913779
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6061.5343313
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.48512276
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.268→1.301 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 783 -
Rwork0.264 14859 -
obs--96.37 %

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