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- PDB-6wuq: Crystal structure of AjiA1 in apo form -

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Basic information

Entry
Database: PDB / ID: 6wuq
TitleCrystal structure of AjiA1 in apo form
ComponentsAjiA1
KeywordsLIGASE / ATP-dependent Ligase
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsPaiva, F.C.R. / Chan, K. / Leadlay, P. / Dias, M.V.B.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation2018/003511 Brazil
Brazilian National Council for Scientific and Technological Development141090/2016-2 Brazil
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2020
Title: The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family
Authors: Paiva, F.C.R. / Chan, K. / Samborskyy, M. / Silber, A.M. / Leadlay, P. / Dias, M.V.B.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AjiA1
B: AjiA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8636
Polymers96,6832
Non-polymers1794
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-45 kcal/mol
Surface area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.777, 128.777, 101.449
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 AjiA1


Mass: 48341.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 35% PEG 300, 100 mM Potassium Citrate Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976195 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976195 Å / Relative weight: 1
ReflectionResolution: 2→48.87 Å / Num. obs: 65461 / % possible obs: 99.8 % / Redundancy: 20.2 % / Biso Wilson estimate: 46.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.015 / Rrim(I) all: 0.069 / Net I/σ(I): 24.4 / Num. measured all: 1320343
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
2-2.0520.72.5739263144830.6880.5762.6371.797.9
9.18-48.8716.80.0271272675710.0070.02895.699.4

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2y27

2y27


Resolution: 2.003→33.816 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.06
RfactorNum. reflection% reflection
Rfree0.2236 3205 4.9 %
Rwork0.1879 --
obs0.1898 65401 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.65 Å2 / Biso mean: 63.5695 Å2 / Biso min: 35.72 Å2
Refinement stepCycle: final / Resolution: 2.003→33.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6693 0 4 152 6849
Biso mean--53.38 58.01 -
Num. residues----859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086879
X-RAY DIFFRACTIONf_angle_d0.9249385
X-RAY DIFFRACTIONf_chiral_restr0.0521042
X-RAY DIFFRACTIONf_plane_restr0.0081235
X-RAY DIFFRACTIONf_dihedral_angle_d20.9474148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0026-2.03250.38921330.35012564269797
2.0325-2.06430.38791180.313227082826100
2.0643-2.09810.34541350.293426782813100
2.0981-2.13430.31741280.274526822810100
2.1343-2.17310.3331300.258426912821100
2.1731-2.21490.27331340.244327232857100
2.2149-2.26010.32361440.232826562800100
2.2601-2.30920.25141410.226227272868100
2.3092-2.36290.25581330.215426572790100
2.3629-2.4220.21191430.212726992842100
2.422-2.48750.24961740.205526552829100
2.4875-2.56060.27511240.210327212845100
2.5606-2.64330.23931250.211727092834100
2.6433-2.73770.2671370.205226922829100
2.7377-2.84730.28661410.214726872828100
2.8473-2.97680.27661300.222527352865100
2.9768-3.13360.2641530.231326832836100
3.1336-3.32980.26821560.211327022858100
3.3298-3.58660.22111400.197827292869100
3.5866-3.9470.2011460.171227062852100
3.947-4.5170.17581670.145227182885100
4.517-5.68660.18281360.153327952931100
5.6866-33.82110.19291370.16128793016100
Refinement TLS params.Method: refined / Origin x: 51.1809 Å / Origin y: 12.875 Å / Origin z: 12.2218 Å
111213212223313233
T0.4991 Å20.0702 Å2-0.0572 Å2-0.3406 Å20.0058 Å2--0.3751 Å2
L0.6347 °2-0.321 °20.0987 °2-0.8478 °20.0451 °2--0.3141 °2
S0.0986 Å °0.1359 Å °-0.0412 Å °-0.1447 Å °-0.0974 Å °0.1389 Å °0.0636 Å °0.0192 Å °0.002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 432
2X-RAY DIFFRACTION1allB4 - 436
3X-RAY DIFFRACTION1allD2 - 4
4X-RAY DIFFRACTION1allS1 - 233
5X-RAY DIFFRACTION1allC1 - 2

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