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- PDB-9bq0: Complex structure of protein crystal of Tri17 with ATP -

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Basic information

Entry
Database: PDB / ID: 9bq0
TitleComplex structure of protein crystal of Tri17 with ATP
ComponentsAMP-binding protein
KeywordsLIGASE / acyl-CoA ligase / AMP-binding domain / N-N bond formation / apo Structure
Function / homologyADENOSINE-5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesStreptomyces tsukubensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionMay 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 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
C: AMP-binding protein
D: AMP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,40114
Polymers246,2274
Non-polymers2,17510
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15140 Å2
ΔGint-90 kcal/mol
Surface area74540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.095, 152.331, 229.642
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
AMP-binding protein / Long-chain fatty acid--CoA ligase


Mass: 61556.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tsukubensis (bacteria) / Gene: B7R87_11280, EWI31_19020 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5H2UY12
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M NaoAC, 25% PEG3350, 0.1mM ATP, 0.2M MgSO4,0.1mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.9→46.44 Å / Num. obs: 68521 / % possible obs: 99.47 % / Redundancy: 10.9 % / Biso Wilson estimate: 55.45 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.06643 / Rrim(I) all: 0.2212 / Net I/σ(I): 8.98
Reflection shellResolution: 2.9→3.004 Å / Rmerge(I) obs: 1.285 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 6771 / CC1/2: 0.857 / Rpim(I) all: 0.4057

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.44 Å / SU ML: 0.4103 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.5201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3298 3407 4.99 %
Rwork0.2783 64810 -
obs0.2809 68217 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.79 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14905 0 130 322 15357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013815381
X-RAY DIFFRACTIONf_angle_d1.559720916
X-RAY DIFFRACTIONf_chiral_restr0.07372326
X-RAY DIFFRACTIONf_plane_restr0.01352681
X-RAY DIFFRACTIONf_dihedral_angle_d17.57185446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.4631300.36472671X-RAY DIFFRACTION99.93
2.94-2.990.4421280.34532706X-RAY DIFFRACTION99.75
2.99-3.030.38731520.33492635X-RAY DIFFRACTION99.75
3.03-3.080.33511470.31982671X-RAY DIFFRACTION99.65
3.08-3.130.3531380.29832694X-RAY DIFFRACTION99.96
3.13-3.190.34811230.3092684X-RAY DIFFRACTION99.79
3.19-3.250.39271240.31652697X-RAY DIFFRACTION99.86
3.25-3.320.36281240.33222703X-RAY DIFFRACTION99.72
3.32-3.390.35341320.29452677X-RAY DIFFRACTION99.72
3.39-3.470.3161420.28612662X-RAY DIFFRACTION99.54
3.47-3.560.31391350.27832686X-RAY DIFFRACTION99.58
3.56-3.650.31881510.2592691X-RAY DIFFRACTION99.86
3.65-3.760.31981500.2532649X-RAY DIFFRACTION99.47
3.76-3.880.26841270.24522713X-RAY DIFFRACTION99.58
3.88-4.020.29631450.24252684X-RAY DIFFRACTION99.65
4.02-4.180.34151600.23662702X-RAY DIFFRACTION99.83
4.18-4.370.29731580.23742691X-RAY DIFFRACTION99.75
4.37-4.60.2851430.23692704X-RAY DIFFRACTION99.58
4.6-4.890.32081510.21762706X-RAY DIFFRACTION99.76
4.89-5.270.3171510.24692716X-RAY DIFFRACTION99.83
5.27-5.80.33411310.26722751X-RAY DIFFRACTION99.76
5.8-6.630.29831640.29872738X-RAY DIFFRACTION99.49
6.63-8.350.33641490.3152785X-RAY DIFFRACTION99.73
8.35-46.440.36711520.3262794X-RAY DIFFRACTION95.19

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