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- PDB-8yyr: Structure of the HitB T293G mutant -

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Basic information

Entry
Database: PDB / ID: 8yyr
TitleStructure of the HitB T293G mutant
ComponentsPutative ATP-dependent b-aminoacyl-ACP synthetase
KeywordsLIGASE / Hitachimycin / polyketide biosynthesis / ATP binding / adenylation
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
AMP-binding / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
: / Putative ATP-dependent b-aminoacyl-ACP synthetase
Similarity search - Component
Biological speciesEmbleya scabrispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, D. / Miyanaga, A. / Chisuga, T. / Kudo, F. / Eguchi, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2024
Title: Engineering the Substrate Specificity of (S)-beta-Phenylalanine Adenylation Enzyme HitB.
Authors: Wang, D. / Miyanaga, A. / Chisuga, T. / Kudo, F. / Eguchi, T.
History
DepositionApr 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ATP-dependent b-aminoacyl-ACP synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2032
Polymers59,6311
Non-polymers5721
Water4,324240
1
A: Putative ATP-dependent b-aminoacyl-ACP synthetase
hetero molecules

A: Putative ATP-dependent b-aminoacyl-ACP synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4064
Polymers119,2612
Non-polymers1,1452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Unit cell
Length a, b, c (Å)67.880, 67.880, 196.654
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative ATP-dependent b-aminoacyl-ACP synthetase


Mass: 59630.648 Da / Num. of mol.: 1 / Mutation: T293G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Embleya scabrispora (bacteria) / Gene: hitB / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7R6G7
#2: Chemical ChemComp-A1L0H / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-(2-bromophenyl)propanoyl]sulfamate


Mass: 572.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22BrN7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 400, calcium acetate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 49771 / % possible obs: 99.9 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.178 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2958 / CC1/2: 0.863

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.264 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2444 4.9 %RANDOM
Rwork0.1767 ---
obs0.1783 47258 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.95 Å2 / Biso mean: 33.616 Å2 / Biso min: 17.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.39 Å20 Å2
2--0.77 Å20 Å2
3----2.5 Å2
Refinement stepCycle: final / Resolution: 1.8→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 35 240 4075
Biso mean--25.14 37.32 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133937
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173764
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.6625364
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5798642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.2919.144222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05215600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.551549
X-RAY DIFFRACTIONr_chiral_restr0.0950.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024459
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02908
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 155 -
Rwork0.237 3462 -
all-3617 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 37.796 Å / Origin y: -31.917 Å / Origin z: -19.784 Å
111213212223313233
T0.0037 Å2-0.0023 Å20.004 Å2-0.0315 Å20.0055 Å2--0.0099 Å2
L0.0817 °2-0.064 °20.0892 °2-0.0515 °2-0.0653 °2--0.374 °2
S-0.0068 Å °-0.0007 Å °0.001 Å °0.0036 Å °0.0019 Å °-0.003 Å °-0.0093 Å °-0.0402 Å °0.0049 Å °

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