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- PDB-8zm7: Engineering omega-amine transaminase for extending substrate scop... -

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Basic information

Entry
Database: PDB / ID: 8zm7
TitleEngineering omega-amine transaminase for extending substrate scope by ancestral sequence reconstruction
ComponentsAmine transaminase
KeywordsTRANSFERASE / homotetramer / PLP-dependent enzyme
Function / homology(2S)-2-hydroxybutanedioic acid
Function and homology information
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuang, J. / Li, N. / Cai, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071268 China
CitationJournal: to be published
Title: Engineering omega-amine transaminase for extending substrate scope by ancestral sequence reconstruction
Authors: Huang, J. / Li, N. / Cai, T.
History
DepositionMay 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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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
C: Amine transaminase
D: Amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,37161
Polymers146,5244
Non-polymers3,84757
Water15,367853
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22790 Å2
ΔGint-529 kcal/mol
Surface area45580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.904, 169.904, 245.079
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11B-693-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Amine transaminase


Mass: 36630.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: branched-chain-amino-acid transaminase

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Non-polymers , 6 types, 910 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.49 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Tris-Hcl pH 7.5 1.5M (NH4)2SO4 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→49.69 Å / Num. obs: 92583 / % possible obs: 99.87 % / Redundancy: 49.69 % / Biso Wilson estimate: 34.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Net I/σ(I): 26.3
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 92583 / CC1/2: 0.999 / % possible all: 99.87

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHASERCCP4 PROGRAM SUITE: 2.8.3 Phaserphasing
XDSJan 10, 2022data scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.69 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 4520 4.88 %
Rwork0.1717 --
obs0.1733 92573 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10039 0 199 853 11091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210438
X-RAY DIFFRACTIONf_angle_d0.4614150
X-RAY DIFFRACTIONf_dihedral_angle_d14.3041439
X-RAY DIFFRACTIONf_chiral_restr0.0451540
X-RAY DIFFRACTIONf_plane_restr0.0041823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.26021480.20672881X-RAY DIFFRACTION100
2.33-2.350.26851640.19972851X-RAY DIFFRACTION100
2.35-2.380.21861270.19812915X-RAY DIFFRACTION100
2.38-2.410.21641440.20112863X-RAY DIFFRACTION100
2.41-2.440.25861700.19162886X-RAY DIFFRACTION100
2.44-2.480.22271500.20632867X-RAY DIFFRACTION100
2.48-2.510.28261410.22622910X-RAY DIFFRACTION100
2.51-2.550.25951320.22372903X-RAY DIFFRACTION100
2.55-2.590.24811610.22452882X-RAY DIFFRACTION100
2.59-2.630.26721300.21442926X-RAY DIFFRACTION100
2.63-2.680.26431430.20932910X-RAY DIFFRACTION100
2.68-2.730.26421430.19842902X-RAY DIFFRACTION100
2.73-2.780.25791440.18872921X-RAY DIFFRACTION100
2.78-2.840.2361580.19432909X-RAY DIFFRACTION100
2.84-2.90.23911660.19542874X-RAY DIFFRACTION100
2.9-2.970.22171530.19782901X-RAY DIFFRACTION100
2.97-3.040.22561390.19392958X-RAY DIFFRACTION100
3.04-3.120.23321600.19862900X-RAY DIFFRACTION100
3.12-3.210.22261570.19312930X-RAY DIFFRACTION100
3.21-3.320.22381580.18662905X-RAY DIFFRACTION100
3.32-3.440.22051560.16772945X-RAY DIFFRACTION100
3.44-3.570.21221430.16612931X-RAY DIFFRACTION100
3.57-3.740.16931490.15292965X-RAY DIFFRACTION100
3.74-3.930.18271500.14612955X-RAY DIFFRACTION100
3.93-4.180.18181590.13962953X-RAY DIFFRACTION100
4.18-4.50.15591640.12492981X-RAY DIFFRACTION100
4.5-4.950.17411550.13212982X-RAY DIFFRACTION100
4.95-5.670.14981370.14823048X-RAY DIFFRACTION100
5.67-7.140.20141370.17813083X-RAY DIFFRACTION100
7.14-49.690.16371820.16663216X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -49.5457 Å / Origin y: 68.5529 Å / Origin z: 12.4159 Å
111213212223313233
T0.1668 Å20.0189 Å20.0006 Å2-0.4372 Å20.0186 Å2--0.2611 Å2
L0.6785 °2-0.3453 °20.2639 °2-0.5163 °2-0.2101 °2--0.4203 °2
S-0.1414 Å °-0.3222 Å °0.0048 Å °0.0779 Å °0.2173 Å °0.0472 Å °-0.0715 Å °-0.1897 Å °-0.0484 Å °
Refinement TLS groupSelection details: all

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