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- PDB-7ypn: Crystal structure of transaminase CC1012 mutant M9 complexed with PLP -

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Basic information

Entry
Database: PDB / ID: 7ypn
TitleCrystal structure of transaminase CC1012 mutant M9 complexed with PLP
ComponentsAspartate aminotransferase family protein
KeywordsTRANSFERASE / Complex / Tranaminase
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding / cytosol
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase family protein
Similarity search - Component
Biological speciesCaulobacter sp. D5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.049 Å
AuthorsYang, L. / Wang, H. / Wei, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Mechanism-Guided Computational Design of omega-Transaminase by Reprograming of High-Energy-Barrier Steps.
Authors: Yang, L. / Zhang, K. / Xu, M. / Xie, Y. / Meng, X. / Wang, H. / Wei, D.
History
DepositionAug 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,7976
Polymers104,1352
Non-polymers6624
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12850 Å2
ΔGint-72 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.734, 78.879, 86.497
Angle α, β, γ (deg.)90.000, 100.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 8 through 351 or resid 353 through 461))
21(chain D and (resid 8 through 351 or resid 353 through 461))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain B and (resid 8 through 351 or resid 353 through 461))
211(chain D and (resid 8 through 351 or resid 353 through 461))

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Components

#1: Protein Aspartate aminotransferase family protein


Mass: 52067.395 Da / Num. of mol.: 2
Mutation: Q25F, D44E, M60W, W64F, Y138F, P192Q, I266A, T377V, A448R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter sp. D5 (bacteria) / Gene: DMC18_08975 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A318BC23
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.69
Details: 100 mM Tris-HCl, pH 8.69, LiCl, 0.8 M, PEG 4000, 29% (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.049→50 Å / Num. obs: 52548 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.24 Å2 / CC1/2: 0.8 / Net I/σ(I): 10.2
Reflection shellResolution: 2.05→2.09 Å / Num. unique obs: 2588 / CC1/2: 0.816 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YPM

7ypm


Resolution: 2.049→39.44 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 2492 5.11 %
Rwork0.1814 46292 -
obs0.183 48784 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.95 Å2 / Biso mean: 24.4227 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 2.049→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6985 0 41 600 7626
Biso mean--23.25 29.73 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027201
X-RAY DIFFRACTIONf_angle_d0.5169751
X-RAY DIFFRACTIONf_chiral_restr0.0431050
X-RAY DIFFRACTIONf_plane_restr0.0041277
X-RAY DIFFRACTIONf_dihedral_angle_d13.944240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B4289X-RAY DIFFRACTION4.308TORSIONAL
12D4289X-RAY DIFFRACTION4.308TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.049-2.08810.2363620.21117242
2.0881-2.13070.252950.2152170161
2.1307-2.17710.25511180.2142203775
2.1771-2.22770.25151420.2166240687
2.2277-2.28340.27431340.2148269696
2.2834-2.34510.24071570.2087272998
2.3451-2.41410.26131470.2074277099
2.4141-2.49210.251520.2041276499
2.4921-2.58110.2541570.202273699
2.5811-2.68440.2121440.19672806100
2.6844-2.80660.26381450.19282805100
2.8066-2.95450.24981500.20032783100
2.9545-3.13950.21321410.1912810100
3.1395-3.38180.21741580.17912799100
3.3818-3.72190.19111490.16422780100
3.7219-4.25990.16681590.15322814100
4.2599-5.36490.16321470.1537281699
5.3649-100.1781350.1668286899

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