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- PDB-7lm0: Crystal structure of GenB3 in complex with PLP -

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Basic information

Entry
Database: PDB / ID: 7lm0
TitleCrystal structure of GenB3 in complex with PLP
ComponentsC-6' aminotransferase
KeywordsBIOSYNTHETIC PROTEIN / PLP-dependent enzyme / gentamicin / biosynthesis
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
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 / C-6' aminotransferase
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBury, P.S. / Huang, F. / Leadlay, P.F. / Dias, M.V.B.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15971-3 Brazil
Sao Paulo Research Foundation (FAPESP)2015/09188-8 Brazil
Sao Paulo Research Foundation (FAPESP)2018/00351-1 Brazil
CitationJournal: Acs Catalysis / Year: 2021
Title: Crystal structure of GenB4 in complex with external aldimine of PLP-sisomicin
Authors: Bury, P.S. / Huang, F. / Leadlay, P.F. / Dias, M.V.B.
History
DepositionFeb 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
A: C-6' aminotransferase
B: C-6' aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8735
Polymers98,2722
Non-polymers6003
Water11,403633
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-47 kcal/mol
Surface area30270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.531, 156.753, 63.893
Angle α, β, γ (deg.)90.000, 115.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C-6' aminotransferase / Glutamate-1-semialdehyde aminotransferase-like protein / GntJ


Mass: 49136.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: gacC, gntJ, genB3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70KE4
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Sodium malonate, pH 4 and 12% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→46.53 Å / Num. obs: 59080 / % possible obs: 95 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Net I/σ(I): 18.6 / Num. measured all: 353510 / Scaling rejects: 127
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
2.09-2.155.30.212273943280.9650.0980.234689.3
9.12-46.536.80.04651497590.9970.0190.0493797.4

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
Aimless0.5.27data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LLD

7lld


Resolution: 2.09→31.08 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 2819 4.78 %
Rwork0.1614 56199 -
obs0.1631 59018 94.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.33 Å2 / Biso mean: 38.7879 Å2 / Biso min: 20.44 Å2
Refinement stepCycle: final / Resolution: 2.09→31.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6881 0 37 633 7551
Biso mean--29.67 46 -
Num. residues----895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087087
X-RAY DIFFRACTIONf_angle_d0.9789623
X-RAY DIFFRACTIONf_chiral_restr0.0581063
X-RAY DIFFRACTIONf_plane_restr0.0061271
X-RAY DIFFRACTIONf_dihedral_angle_d19.2131008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.130.29171400.2232592273287
2.13-2.170.281330.20062745287895
2.17-2.210.26691430.18862769291292
2.21-2.250.23621460.18292669281593
2.25-2.30.23171290.18542722285191
2.3-2.360.26251240.17392769289393
2.36-2.420.24751350.17682774290995
2.42-2.480.2221350.17492813294895
2.48-2.550.21161310.16212844297596
2.55-2.640.19491330.1622819295295
2.64-2.730.19481260.1652838296496
2.73-2.840.22011750.17282789296495
2.84-2.970.23141400.17032866300696
2.97-3.130.20811360.16832834297095
3.13-3.320.20291010.16562908300997
3.32-3.580.19011650.15982852301798
3.58-3.940.17071540.14792891304597
3.94-4.510.16431560.13262890304698
4.51-5.670.16441610.15442869303097
5.67-31.080.18951560.16442946310298
Refinement TLS params.Method: refined / Origin x: 77.0536 Å / Origin y: 35.5115 Å / Origin z: 19.0588 Å
111213212223313233
T0.1882 Å20.0019 Å2-0.0045 Å2-0.2449 Å20.0218 Å2--0.1848 Å2
L0.583 °20.2877 °20.0924 °2-1.5202 °20.2604 °2--0.3899 °2
S-0.0144 Å °0.0875 Å °0.0658 Å °-0.1655 Å °0.0146 Å °0.0354 Å °-0.0246 Å °-0.0068 Å °-0.0059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 506
2X-RAY DIFFRACTION1allB5 - 450
3X-RAY DIFFRACTION1allS1 - 657
4X-RAY DIFFRACTION1allC1 - 2

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