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- PDB-4uug: The (R)-selective amine transaminase from Aspergillus fumigatus w... -

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Basic information

Entry
Database: PDB / ID: 4uug
TitleThe (R)-selective amine transaminase from Aspergillus fumigatus with inhibitor bound
ComponentsAMINE TRANSAMINASE
KeywordsTRANSFERASE / GABACULINE
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
FORMIC ACID / 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID / Branched-chain amino acid aminotransferase, putative
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsThomsen, M. / Hinrichs, W.
Citation
Journal: FEBS J. / Year: 2015
Title: Structural and Biochemical Characterization of the Dual Substrate Recognition of the (R)-Selective Amine Transaminase from Aspergillus Fumigatus
Authors: Skalden, L. / Thomsen, M. / Hohne, M. / Bornscheuer, U.T. / Hinrichs, W.
#1: 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. / Hoehne, M. / Bornscheuer, U.T. / Hinrichs, W.
History
DepositionJul 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2May 4, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / diffrn_detector ...database_2 / diffrn_detector / pdbx_database_status / 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 / _diffrn_detector.pdbx_collection_date / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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_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
Revision 1.3Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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: AMINE TRANSAMINASE
B: AMINE TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,65713
Polymers74,3852
Non-polymers1,27211
Water14,304794
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-33.9 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.449, 144.449, 96.112
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2149-

HOH

21B-2125-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99995, 0.00984, 0.00071), (0.00936, 0.92322, 0.38416), (0.00313, 0.38415, -0.92327)
Vector: 159.38164, -13.08294, 61.27308)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AMINE TRANSAMINASE / 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, branched-chain-amino-acid transaminase

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Non-polymers , 6 types, 805 molecules

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


Mass: 368.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N2O7P
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 4 Å3/Da / Density % sol: 69.3 % / Description: NONE
Crystal growpH: 4.6 / Details: 2.0 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2014 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.6→47.28 Å / Num. obs: 151504 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CHI

4chi


Resolution: 1.6→47.25 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.404 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.14811 7614 5 %RANDOM
Rwork0.13376 ---
obs0.13448 143859 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 85 794 5929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195894
X-RAY DIFFRACTIONr_bond_other_d0.0010.025646
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9858102
X-RAY DIFFRACTIONr_angle_other_deg0.8762.99913080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7445794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23423.832274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.577151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1811545
X-RAY DIFFRACTIONr_chiral_restr0.1040.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216821
X-RAY DIFFRACTIONr_gen_planes_other0.010.021370
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_it1.3061.192812
X-RAY DIFFRACTIONr_mcbond_other1.3061.192813
X-RAY DIFFRACTIONr_mcangle_it1.9831.7793558
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1071.4523082
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 564 -
Rwork0.224 10566 -
obs--99.84 %
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)
10.2337-0.01480.06310.38010.22820.18310.00850.0341-0.0228-0.0836-0.04430.0211-0.0262-0.00230.03580.10440.01880.00360.0639-0.00720.054474.387-27.69810.895
21.0210.46150.18920.60460.1281.8573-0.02960.0877-0.11160.02940.0021-0.22820.07340.24320.02750.04060.030900.0860.01920.103197.294-24.53123.88
30.1236-0.0923-0.09180.43480.19860.24770.0208-0.0044-0.0055-0.1061-0.07630.0649-0.0461-0.02250.05550.08750.0257-0.02970.0542-0.01690.055965.671-9.17515.79
40.79280.9513-0.8943.4573.4239.7577-0.0525-0.0568-0.07420.1285-0.1729-0.01470.4095-0.10540.22540.11030.0021-0.01310.067-0.00820.041970.864-15.78216.208
50.2450.0290.15620.4413-0.09760.2177-0.0057-0.0148-0.02540.0108-0.0575-0.05780.0277-0.00530.06320.06990.00040.01020.05710.02190.072285.056-33.78841.223
60.1952-0.19250.41522.1146-2.30942.7614-0.0802-0.11890.0407-0.25040.16690.14320.1474-0.2896-0.08680.12610.0053-0.0420.12940.01110.086463.081-31.76829.627
70.12150.1184-0.06930.4574-0.12180.21510.0173-0.0156-0.01550.0601-0.0683-0.0839-0.02380.02280.0510.0607-0.0139-0.02420.06430.0280.06893.623-14.85443.681
82.8366-0.9886-2.21873.6284-0.08712.85460.0695-0.0382-0.1644-0.1577-0.1863-0.06530.02490.24390.11680.07090.0127-0.0090.06920.01850.056988.58-20.89940.451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 122
2X-RAY DIFFRACTION2A123 - 136
3X-RAY DIFFRACTION3A137 - 321
4X-RAY DIFFRACTION4A400 - 401
5X-RAY DIFFRACTION5B1 - 122
6X-RAY DIFFRACTION6B123 - 136
7X-RAY DIFFRACTION7B137 - 321
8X-RAY DIFFRACTION8B400 - 401

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