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- PDB-8tf7: Apo structure of protein crystal of Tri17 -

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Basic information

Entry
Database: PDB / ID: 8tf7
TitleApo structure of protein crystal of Tri17
ComponentsAMP-binding protein
KeywordsLIGASE / acyl-CoA ligase / AMP-binding domain / N-N bond formation / apo Structure
Function / homology:
Function and homology information
Biological speciesStreptomyces tsukubensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZhai, R. / Zhang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM136758 United States
CitationJournal: Nat.Chem. / Year: 2024
Title: Enzymatic synthesis of azide by a promiscuous N-nitrosylase.
Authors: Del Rio Flores, A. / Zhai, R. / Kastner, D.W. / Seshadri, K. / Yang, S. / De Matias, K. / Shen, Y. / Cai, W. / Narayanamoorthy, M. / Do, N.B. / Xue, Z. / Marzooqi, D.A. / Kulik, H.J. / Zhang, W.
History
DepositionJul 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMP-binding protein
B: AMP-binding protein


Theoretical massNumber of molelcules
Total (without water)123,7582
Polymers123,7582
Non-polymers00
Water4,918273
1
A: AMP-binding protein
B: AMP-binding protein

A: AMP-binding protein
B: AMP-binding protein


Theoretical massNumber of molelcules
Total (without water)247,5164
Polymers247,5164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area10530 Å2
ΔGint-34 kcal/mol
Surface area80930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.992, 105.992, 235.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein AMP-binding protein


Mass: 61878.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tsukubensis (bacteria) / Gene: B7R87_11280 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5H2UY12
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG3350, 100 mM KSCN, 100 mM Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.45→48.34 Å / Num. obs: 50341 / % possible obs: 100 % / Redundancy: 18.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.044 / Rrim(I) all: 0.191 / Χ2: 1 / Net I/σ(I): 17.6 / Num. measured all: 937072
Reflection shellResolution: 2.45→2.53 Å / % possible obs: 100 % / Redundancy: 19.3 % / Rmerge(I) obs: 1.665 / Num. measured all: 88254 / Num. unique obs: 4566 / CC1/2: 0.71 / Rpim(I) all: 0.388 / Rrim(I) all: 1.71 / Χ2: 0.99 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→48.34 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 2524 5.02 %
Rwork0.2156 --
obs0.2179 50258 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7966 0 0 273 8239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038158
X-RAY DIFFRACTIONf_angle_d0.59711105
X-RAY DIFFRACTIONf_dihedral_angle_d16.0492915
X-RAY DIFFRACTIONf_chiral_restr0.0431242
X-RAY DIFFRACTIONf_plane_restr0.0041447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.50.34351280.29372627X-RAY DIFFRACTION100
2.5-2.550.31531450.28482579X-RAY DIFFRACTION100
2.55-2.60.32921410.2942605X-RAY DIFFRACTION100
2.6-2.660.32691320.28692622X-RAY DIFFRACTION100
2.66-2.730.3881380.28152602X-RAY DIFFRACTION100
2.73-2.80.32611370.2722617X-RAY DIFFRACTION100
2.8-2.890.31451510.25562605X-RAY DIFFRACTION100
2.89-2.980.27781450.24952600X-RAY DIFFRACTION100
2.98-3.090.31311350.23852621X-RAY DIFFRACTION100
3.09-3.210.28011500.24542646X-RAY DIFFRACTION100
3.21-3.360.27581300.23772631X-RAY DIFFRACTION100
3.36-3.530.25491330.22142672X-RAY DIFFRACTION100
3.53-3.750.23811320.19592643X-RAY DIFFRACTION100
3.75-4.040.24571500.18252646X-RAY DIFFRACTION100
4.04-4.450.21311470.17082677X-RAY DIFFRACTION100
4.45-5.090.19631360.16072703X-RAY DIFFRACTION100
5.09-6.420.22861430.1982739X-RAY DIFFRACTION100
6.42-48.340.24921510.20352899X-RAY DIFFRACTION100

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