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- PDB-7ypm: Crystal structure of transaminase CC1012 complexed with PLP and L... -

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Basic information

Entry
Database: PDB / ID: 7ypm
TitleCrystal structure of transaminase CC1012 complexed with PLP and L-alanine
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
ALANINE / 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: 1.984 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

Downloads & links

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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)209,46416
Polymers207,7734
Non-polymers1,69112
Water23,2031288
1
A: Aspartate aminotransferase family protein
hetero molecules

C: Aspartate aminotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7278
Polymers103,8872
Non-polymers8416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area12740 Å2
ΔGint-71 kcal/mol
Surface area25800 Å2
MethodPISA
2
B: Aspartate aminotransferase family protein
D: Aspartate aminotransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7378
Polymers103,8872
Non-polymers8516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-78 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.968, 79.272, 173.845
Angle α, β, γ (deg.)90.000, 100.310, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 502)
21(chain B and resid 502)
31(chain D and resid 502)
41(chain D and resid 503)
51(chain B and resid 503)
61(chain C and resid 503)
12(chain A and (resid 8 through 420 or resid 422 through 461))
22(chain B and (resid 8 through 420 or resid 422 through 461))
32(chain C and (resid 8 through 420 or resid 422 through 461))
42(chain D and (resid 8 through 420 or resid 422 through 461))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and resid 502)
211(chain B and resid 502)
311(chain D and resid 502)
411(chain D and resid 503)
511(chain B and resid 503)
611(chain C and resid 503)
112(chain A and (resid 8 through 420 or resid 422 through 461))
122(chain A and (resid 8 through 420 or resid 422 through 461))
212(chain B and (resid 8 through 420 or resid 422 through 461))
222(chain B and (resid 8 through 420 or resid 422 through 461))
312(chain C and (resid 8 through 420 or resid 422 through 461))
322(chain C and (resid 8 through 420 or resid 422 through 461))
412(chain D and (resid 8 through 420 or resid 422 through 461))
422(chain D and (resid 8 through 420 or resid 422 through 461))

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aspartate aminotransferase family protein


Mass: 51943.254 Da / Num. of mol.: 4 / Mutation: D44E, Y138F, P192Q, 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

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Non-polymers , 5 types, 1300 molecules

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


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


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


Mass: 18.015 Da / Num. of mol.: 1288 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.69
Details: 100 mM Tris-HCl, pH 8.69, 0.8 M LiCl, 29% (w/v) PEG 4000

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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 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.984→50 Å / Num. obs: 117255 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.936 / Net I/σ(I): 11.762
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 5815 / CC1/2: 0.936 / CC star: 0.983 / % possible all: 99.9

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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: 6GWI

6gwi


Resolution: 1.984→46.606 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 5909 5.05 %
Rwork0.216 111030 -
obs0.2171 116939 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.33 Å2 / Biso mean: 26.501 Å2 / Biso min: 10.1 Å2
Refinement stepCycle: final / Resolution: 1.984→46.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13944 0 107 1288 15339
Biso mean--28.99 35.17 -
Num. residues----1816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314380
X-RAY DIFFRACTIONf_angle_d0.77619472
X-RAY DIFFRACTIONf_chiral_restr0.0482107
X-RAY DIFFRACTIONf_plane_restr0.0042552
X-RAY DIFFRACTIONf_dihedral_angle_d5.4459297
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6X-RAY DIFFRACTION5.159TORSIONAL
12B6X-RAY DIFFRACTION5.159TORSIONAL
13D6X-RAY DIFFRACTION5.159TORSIONAL
14D6X-RAY DIFFRACTION5.159TORSIONAL
15B6X-RAY DIFFRACTION5.159TORSIONAL
16C6X-RAY DIFFRACTION5.159TORSIONAL
21A8693X-RAY DIFFRACTION5.159TORSIONAL
22B8693X-RAY DIFFRACTION5.159TORSIONAL
23C8693X-RAY DIFFRACTION5.159TORSIONAL
24D8693X-RAY DIFFRACTION5.159TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9843-2.00680.34241650.3024257570
2.0068-2.03040.37052110.29883734100
2.0304-2.05520.30212220.29533678100
2.0552-2.08120.2792060.27673729100
2.0812-2.10860.27311860.25443688100
2.1086-2.13750.28891780.24773798100
2.1375-2.1680.26081750.24183708100
2.168-2.20040.24271930.24413775100
2.2004-2.23480.26852150.24543643100
2.2348-2.27140.25262000.23553755100
2.2714-2.31060.25111740.22723760100
2.3106-2.35260.22991990.22473748100
2.3526-2.39780.2621750.22853738100
2.3978-2.44680.28551950.21713724100
2.4468-2.50.26171860.21643726100
2.5-2.55810.23992010.21243788100
2.5581-2.62210.26811520.21313741100
2.6221-2.6930.21421940.20693727100
2.693-2.77220.23281950.20423757100
2.7722-2.86170.24311880.20953730100
2.8617-2.96390.21562220.20863714100
2.9639-3.08260.22632330.19623730100
3.0826-3.22290.21712220.19493709100
3.2229-3.39270.2161920.19213760100
3.3927-3.60520.20061870.19783758100
3.6052-3.88350.1932040.18833739100
3.8835-4.2740.18622020.19543788100
4.274-4.89190.24061880.19963786100
4.8919-6.1610.25542090.22163767100
6.161-46.6060.25192400.2361375797

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