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- PDB-6snu: Crystal structure of the W60C mutant of the (S)-selective transam... -

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Basic information

Entry
Database: PDB / ID: 6snu
TitleCrystal structure of the W60C mutant of the (S)-selective transaminase from Chromobacterium violaceum
ComponentsAspartate aminotransferase family protein
KeywordsTRANSFERASE / Transaminase / PLP / Trp60Cys / W60C / Chromobacterium violaceum / Complex / Mutant
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding
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 / Pyridoxal phosphate-dependent transferase ...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
PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase family protein
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsRuggieri, F. / Gustafsson, C. / Kimbung, R.Y. / Walse, B. / Logan, D.T. / Berglund, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
European Union634200 Sweden
CitationJournal: Not Published
Title: Crystal Structures Combined with Molecular Dynamics Reveal Altered Flow of Water in the Active Site of W60C Chromobacterium violaceum omega-transaminase
Authors: Ruggieri, F. / Gustafsson, C. / Kimbung, R.Y. / Walse, B. / Logan, D.T. / Berglund, P.
History
DepositionAug 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _database_2.pdbx_DOI ..._citation.journal_abbrev / _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

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Assembly

Deposited unit
A: Aspartate aminotransferase family protein
B: Aspartate aminotransferase family protein
C: Aspartate aminotransferase family protein
D: Aspartate aminotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,52912
Polymers208,2924
Non-polymers1,2378
Water4,125229
1
A: Aspartate aminotransferase family protein
B: Aspartate aminotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8898
Polymers104,1462
Non-polymers7436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-60 kcal/mol
Surface area28170 Å2
MethodPISA
2
C: Aspartate aminotransferase family protein
D: Aspartate aminotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6414
Polymers104,1462
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-69 kcal/mol
Surface area28060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.221, 62.196, 118.423
Angle α, β, γ (deg.)75.030, 81.310, 75.300
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA5 - 45511 - 461
21ALAALABB5 - 45511 - 461
12ALAALAAA5 - 45511 - 461
22ALAALACC5 - 45511 - 461
13ALAALAAA5 - 45511 - 461
23ALAALADD5 - 45511 - 461
14ARGARGBB5 - 45611 - 462
24ARGARGCC5 - 45611 - 462
15ARGARGBB5 - 45611 - 462
25ARGARGDD5 - 45611 - 462
16GLYGLYCC5 - 45711 - 463
26GLYGLYDD5 - 45711 - 463

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Aspartate aminotransferase family protein / L-Lysine-8-amino-7-oxononanoate aminotransferase


Mass: 52073.113 Da / Num. of mol.: 4 / Mutation: W60C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: bioK, CBW21_20070, NCTC8684_01926 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1R0MXM9, Transferases; Transferring nitrogenous groups; Transaminases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 22.5 % w/v PEG 4000, 350 mM NaCl, 0.1 mM PLP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.00964 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 2015
RadiationMonochromator: bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00964 Å / Relative weight: 1
ReflectionResolution: 1.8→50.51 Å / Num. obs: 145405 / % possible obs: 96.5 % / Redundancy: 3.9 % / CC1/2: 0.985 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.105 / Rrim(I) all: 0.208 / Net I/σ(I): 13.3 / Num. measured all: 568888 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.833.91.1872759070700.2380.6941.3762.495
9.86-50.513.80.05734039010.9930.0340.06738.498.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Rotation7.53 Å48.23 Å
Translation7.53 Å48.23 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0253refinement
XDSdata reduction
Aimless0.5.17data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A6T

4a6t


Resolution: 2→48.28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.1946 / WRfactor Rwork: 0.1646 / FOM work R set: 0.8456 / SU B: 9.678 / SU ML: 0.122 / SU R Cruickshank DPI: 0.2197 / SU Rfree: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 5299 5 %RANDOM
Rwork0.1813 ---
obs0.183 100404 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.62 Å2 / Biso mean: 20.599 Å2 / Biso min: 6.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0.01 Å2-0.03 Å2
2---0.02 Å20.01 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14297 0 16 229 14542
Biso mean--39.67 18.14 -
Num. residues----1814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01314703
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713422
X-RAY DIFFRACTIONr_angle_refined_deg1.841.64319904
X-RAY DIFFRACTIONr_angle_other_deg1.4531.57630972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24451812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.37221.019824
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.531152342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.01615122
X-RAY DIFFRACTIONr_chiral_restr0.0950.21801
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023418
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A149970.07
12B149970.07
21A149930.07
22C149930.07
31A149500.07
32D149500.07
41B150050.08
42C150050.08
51B150580.06
52D150580.06
61C150500.07
62D150500.07
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 361 -
Rwork0.282 7119 -
all-7480 -
obs--92.21 %
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)
10.96030.5024-0.35741.16230.03990.92830.0977-0.06610.2270.0527-0.01920.0881-0.15290.0366-0.07860.0794-0.01720.00280.0985-0.02930.0865-24.860617.532852.7071
21.11460.2053-0.11820.49120.29751.09950.0156-0.10060.01180.03130.0126-0.06690.06560.1487-0.02820.049-0.0091-0.01570.06920.01270.0513-9.71977.236626.5331
30.53730.0917-0.0561.06080.28230.5645-0.0151-0.01410.03590.0450.02190.03530.0013-0.0313-0.00680.029-0.0031-0.01070.00550.00310.0084-25.477935.9469-4.9997
40.75350.10670.11660.78950.22510.72890.01160.0722-0.1193-0.10550.0494-0.18520.09280.1176-0.0610.0767-0.00430.01390.0398-0.01240.0585-10.661221.6934-29.3558
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 501
2X-RAY DIFFRACTION2B5 - 701
3X-RAY DIFFRACTION3C5 - 459
4X-RAY DIFFRACTION4D5 - 458

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