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- PDB-7xh4: Dihydrofolate Reductase-like Protein SacH in safracin biosynthesi... -

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Basic information

Entry
Database: PDB / ID: 7xh4
TitleDihydrofolate Reductase-like Protein SacH in safracin biosynthesis complex with safracin A
ComponentsUncharacterized protein sfcH
KeywordsOXIDOREDUCTASE / reductase / safracin biosynthesis / self-resistance / complex structure.
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / nucleotide binding
Similarity search - Function
: / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Safracin A / Chem-NDP / Uncharacterized protein sfcH
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMa, X. / Shao, N. / Zhang, Y. / Yang, D. / Ma, M. / Tang, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Pharm Sin B / Year: 2023
Title: Dihydrofolate reductase-like protein inactivates hemiaminal pharmacophore for self-resistance in safracin biosynthesis.
Authors: Shao, N. / Ma, X. / Zhang, Y.Y. / Yang, D. / Ma, M. / Tang, G.L.
History
DepositionApr 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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
A: Uncharacterized protein sfcH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2893
Polymers22,0191
Non-polymers1,2702
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-3 kcal/mol
Surface area9110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.727, 68.727, 157.286
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Uncharacterized protein sfcH / SacH


Mass: 22018.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5JCL3
#2: Chemical ChemComp-EN7 / Safracin A


Mass: 524.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H36N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 28% (w/v) PEG 1500, 100mM PCB buffer pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.2→29.76 Å / Num. obs: 11851 / % possible obs: 99.7 % / Redundancy: 20 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 55.28
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.496 / Num. unique obs: 1186

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XW7

2xw7


Resolution: 2.2→29.76 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2821 1177 9.98 %
Rwork0.2342 10613 -
obs0.239 11790 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.84 Å2 / Biso mean: 34.9333 Å2 / Biso min: 16.02 Å2
Refinement stepCycle: final / Resolution: 2.2→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 86 69 1514
Biso mean--36.6 36.57 -
Num. residues----177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.30.35781440.307412871431100
2.3-2.420.40521410.303812781419100
2.42-2.570.37021420.304112931435100
2.57-2.770.34051440.30061300144499
2.77-3.050.32271440.275113091453100
3.05-3.490.32061480.235213301478100
3.49-4.40.23621510.197313551506100
4.4-29.760.20941630.185214611624100

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