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- PDB-5g2q: The crystal structure of a S-selective transaminase from Arthroba... -

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Basic information

Entry
Database: PDB / ID: 5g2q
TitleThe crystal structure of a S-selective transaminase from Arthrobacter sp. with alanine bound
ComponentsTRANSAMINASE
KeywordsTRANSFERASE / TRANSAMINASE
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding / cytosol
Similarity search - Function
: / 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 ...: / 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
Chem-PDA / Transaminase
Similarity search - Component
Biological speciesARTHROBACTER SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Authorsvan Oosterwijk, N. / Willies, S. / Hekelaar, J. / Terwisscha van Scheltinga, A.C. / Turner, N.J. / Dijkstra, B.W.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Basis of Substrate Range and Enantioselectivity of Two S-Selective Omega- Transaminases
Authors: Van Oosterwijk, N. / Willies, S. / Hekelaar, J. / Terwisscha Van Scheltinga, A.C. / Turner, N.J. / Dijkstra, B.W.
History
DepositionApr 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSAMINASE
B: TRANSAMINASE
C: TRANSAMINASE
D: TRANSAMINASE
E: TRANSAMINASE
F: TRANSAMINASE
G: TRANSAMINASE
H: TRANSAMINASE
I: TRANSAMINASE
J: TRANSAMINASE
K: TRANSAMINASE
L: TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)654,28124
Polymers650,43812
Non-polymers3,84312
Water14,232790
1
E: TRANSAMINASE
F: TRANSAMINASE
G: TRANSAMINASE
H: TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,0948
Polymers216,8134
Non-polymers1,2814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27390 Å2
ΔGint-156.9 kcal/mol
Surface area56270 Å2
MethodPISA
2
I: TRANSAMINASE
J: TRANSAMINASE
K: TRANSAMINASE
L: TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,0948
Polymers216,8134
Non-polymers1,2814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27450 Å2
ΔGint-158.9 kcal/mol
Surface area57140 Å2
MethodPISA
3
A: TRANSAMINASE
B: TRANSAMINASE
C: TRANSAMINASE
D: TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,0948
Polymers216,8134
Non-polymers1,2814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27290 Å2
ΔGint-154.3 kcal/mol
Surface area56800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.278, 99.814, 217.337
Angle α, β, γ (deg.)81.58, 89.12, 74.49
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
TRANSAMINASE


Mass: 54203.145 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL-5'-PHOSPHATE COVALENTLY BOUND ALANINE / Source: (gene. exp.) ARTHROBACTER SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41
References: UniProt: A0A1C7D191*PLUS, Transferases; Transferring nitrogenous groups; Transaminases
#2: Chemical
ChemComp-PDA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID / PYRIDOXYL-ALANINE-5-PHOSPHATE


Mass: 320.236 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C11H17N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsALANINE COVALENTLY BOUND TO PYRIDOXAL-5'-PHOSPHATE (PLA): ALANINE COVALENTLY BOUND TO PYRIDOXAL-5'-PHOSPHATE

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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: 2.09 Å3/Da / Density % sol: 41.25 % / Description: NONE
Crystal growpH: 5
Details: 15% PEG 3350 0.2 M NA-MALONATE 100 MM MMT BUFFER (DL-MALIC ACID, MES AND TRIS BASE) PH 5.0, 10 MM PLP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.71
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.71 Å / Relative weight: 1
ReflectionResolution: 2.3→43 Å / Num. obs: 214456 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.8 / % possible all: 87.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GJU

3gju


Resolution: 2.3→47.96 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 10758 5 %RANDOM
Rwork0.1916 ---
obs-203694 93.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43519 0 252 790 44561
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)
11.2533-0.24950.00120.5831-0.22040.85670.072-0.16940.12210.1891-0.03510.0308-0.08990.0009-0.03690.62940.34720.15180.30210.05810.0556-31.01238.00950.502
21.10510.0082-0.30691.0693-0.07130.76090.08670.2514-0.0102-0.1884-0.0613-0.04470.01510.0668-0.02540.59850.43510.14040.37260.09060.0358-24.06727.96121.315
31.1787-0.21550.11660.74010.07980.6818-0.0015-0.3455-0.15850.2440.0154-0.0134-0.00030.0973-0.01390.64420.37140.11690.42120.1690.1322-10.82-0.70968.141
41.0480.037-0.07741.2416-0.12560.75270.06240.1086-0.3855-0.168-0.07950.0790.16210.06410.01710.62280.43350.11440.30920.06120.2621-11.223-13.59339.098
50.84160.2073-0.25931.2629-0.21261.01310.05910.38910.1177-0.3721-0.00670.1123-0.0683-0.0016-0.05240.75460.43890.08260.59310.14270.1179-25.619-7.633-51.154
61.5105-0.2666-0.0520.8056-0.15640.86220.0726-0.03160.34290.1319-0.01690.1759-0.2285-0.0628-0.05570.70710.4110.18950.3250.06770.292-26.7724.291-21.704
70.97050.6550.13781.92020.01240.93-0.05520.3515-0.2681-0.28450.1395-0.0880.15370.0704-0.08430.69460.45040.13460.4593-0.00160.1138-9.982-48.486-33.202
81.4580.3390.38651.50970.23820.82080.1389-0.1256-0.03030.4091-0.0778-0.1441-0.02180.1003-0.0610.73110.38990.0990.35090.09480.0449-4.379-33.746-5.841
91.61920.88540.2732.41790.46520.7706-0.11590.4566-0.239-0.44050.2441-0.3549-0.05310.0595-0.12820.72850.34020.22890.5834-0.07940.2012-26.673-42.75192.655
101.87560.10390.20811.25710.29420.75130.2615-0.2996-0.43980.5735-0.1311-0.46690.24350.0684-0.13030.94930.295-0.03450.50620.13150.442-20.233-52.683121.878
112.07871.81720.62933.79511.10251.0631-0.0184-0.00661.1427-0.251-0.23111.1073-0.34-0.11560.24950.77390.40040.16420.4465-0.03880.8264-40.004-1.074109.951
122.06891.07610.09472.24250.3690.80010.6168-0.85870.62261.1915-0.82340.63430.1828-0.28020.20661.3875-0.07090.54520.9943-0.4030.3849-40.766-13.98139.014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 1000
2X-RAY DIFFRACTION2B7 - 1000
3X-RAY DIFFRACTION3C7 - 1000
4X-RAY DIFFRACTION4D7 - 1000
5X-RAY DIFFRACTION5E7 - 1000
6X-RAY DIFFRACTION6F7 - 1000
7X-RAY DIFFRACTION7G7 - 1000
8X-RAY DIFFRACTION8H7 - 1000
9X-RAY DIFFRACTION9I7 - 1000
10X-RAY DIFFRACTION10J7 - 1000
11X-RAY DIFFRACTION11K7 - 1000
12X-RAY DIFFRACTION12L8 - 1000

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