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- PDB-4za1: Crystal Structure of NosA Involved in Nosiheptide Biosynthesis -

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Basic information

Entry
Database: PDB / ID: 4za1
TitleCrystal Structure of NosA Involved in Nosiheptide Biosynthesis
ComponentsNosA
KeywordsTRANSFERASE / beta barrel
Function / homologyAlpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / NosA
Function and homology information
Biological speciesStreptomyces actuosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLiu, S. / Guo, H. / Zhang, T. / Han, L. / Yao, P. / Zhang, Y. / Rong, N. / Yu, Y. / Lan, W. / Wang, C. ...Liu, S. / Guo, H. / Zhang, T. / Han, L. / Yao, P. / Zhang, Y. / Rong, N. / Yu, Y. / Lan, W. / Wang, C. / Ding, J. / Wang, R. / Liu, W. / Cao, C.
CitationJournal: Sci Rep / Year: 2015
Title: Structure-based Mechanistic Insights into Terminal Amide Synthase in Nosiheptide-Represented Thiopeptides Biosynthesis
Authors: Liu, S. / Guo, H. / Zhang, T. / Han, L. / Yao, P. / Zhang, Y. / Rong, N. / Yu, Y. / Lan, W. / Wang, C. / Ding, J. / Wang, R. / Liu, W. / Cao, C.
History
DepositionApr 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Other
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NosA
B: NosA
C: NosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0614
Polymers48,9073
Non-polymers1541
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-12 kcal/mol
Surface area15870 Å2
Unit cell
Length a, b, c (Å)143.371, 143.371, 143.371
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein NosA


Mass: 16302.233 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces actuosus (bacteria) / Gene: nosA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C6FX40
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG 5100 / PH range: 6.0 - 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 18105 / % possible obs: 100 % / Redundancy: 81.9 % / Rmerge(I) obs: 0.092 / Χ2: 1.243 / Net I/av σ(I): 87.136 / Net I/σ(I): 12 / Num. measured all: 1483177
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.5981.80.46417651.002100
2.59-2.69820.3817591.141100
2.69-2.8282.70.2417781.025100
2.82-2.9683.30.18817651.015100
2.96-3.1583.50.12517741.045100
3.15-3.3984.20.0917981.12100
3.39-3.7383.60.0917941.492100
3.73-4.2782.30.0918202.16100
4.27-5.3880.20.07218521.484100
5.38-5076.20.04120000.93299.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.215 913 -
Rwork0.179 --
obs0.263 17056 100 %
Displacement parametersBiso max: 157.53 Å2 / Biso mean: 48.4845 Å2 / Biso min: 7.29 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 8 128 2343
Refine LS restraintsType: r_bond_refined_d / Dev ideal: 0.007

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