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- PDB-4fqd: Crystal structure of the enolpyruvyl transferase NikO from Strept... -

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Basic information

Entry
Database: PDB / ID: 4fqd
TitleCrystal structure of the enolpyruvyl transferase NikO from Streptomyces tendae
ComponentsNikO protein
KeywordsTRANSFERASE / beta/alpha inverse barrel / enolpyruvyl transferase / fosfomycin binding
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytoplasm
Similarity search - Function
: / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesStreptomyces tendae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOberdorfer, G. / Gruber, K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and functional characterization of NikO, an enolpyruvyl transferase essential in nikkomycin biosynthesis.
Authors: Oberdorfer, G. / Binter, A. / Ginj, C. / Macheroux, P. / Gruber, K.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NikO protein
B: NikO protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1515
Polymers102,8632
Non-polymers2883
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NikO protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6233
Polymers51,4311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: NikO protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5272
Polymers51,4311
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.210, 120.050, 153.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 13:93 or resseq 97:126 or resseq 140:157 or resseq 159:458 )
211chain 'B' and (resseq 13:93 or resseq 97:126 or resseq 140:157 or resseq 159:458 )

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Components

#1: Protein NikO protein


Mass: 51431.340 Da / Num. of mol.: 2 / Mutation: P52R, D96E, V97L, V141D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tendae (bacteria) / Gene: nikO / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q712I1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 6.5
Details: 0.2 M Li Sulfate, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350, Microbatch, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2010
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→51.07 Å / Num. all: 31067 / Num. obs: 28377 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 20.22 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6.6 / % possible all: 91.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2yvw

2yvw


Resolution: 2.5→47.248 Å / SU ML: 0.72 / σ(F): 1.35 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 1428 5.03 %RANDOM
Rwork0.1953 ---
all0.1953 31067 --
obs0.1972 28375 91.36 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.336 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2376 Å20 Å2-0 Å2
2--0.7895 Å2-0 Å2
3----5.0272 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6575 0 15 339 6929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026754
X-RAY DIFFRACTIONf_angle_d0.6319235
X-RAY DIFFRACTIONf_dihedral_angle_d11.9782434
X-RAY DIFFRACTIONf_chiral_restr0.0391089
X-RAY DIFFRACTIONf_plane_restr0.0031206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3223X-RAY DIFFRACTIONPOSITIONAL
12B3223X-RAY DIFFRACTIONPOSITIONAL0.639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58940.31881580.24022927X-RAY DIFFRACTION100
2.5894-2.69310.328960.2351837X-RAY DIFFRACTION64
2.6931-2.81560.27791560.22962924X-RAY DIFFRACTION100
2.8156-2.9640.27481490.21992927X-RAY DIFFRACTION100
2.964-3.14970.23991650.20482905X-RAY DIFFRACTION100
3.1497-3.39280.22851440.20792945X-RAY DIFFRACTION100
3.3928-3.73410.23151050.18921918X-RAY DIFFRACTION65
3.7341-4.27420.22651230.17552505X-RAY DIFFRACTION84
4.2742-5.38380.17671870.15542949X-RAY DIFFRACTION100
5.3838-47.25650.19681450.18133110X-RAY DIFFRACTION100

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