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- PDB-5wpi: The virulence-associated protein HsvA from the fire blight pathog... -

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Basic information

Entry
Database: PDB / ID: 5wpi
TitleThe virulence-associated protein HsvA from the fire blight pathogen Erwinia amylovora is a polyamine amidinotransferase
ComponentsHsvA
KeywordsTRANSFERASE / amidinotransferase
Function / homologyamidinotransferase activity / Glycine/inosamine-phosphate amidinotransferase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta / HsvA
Function and homology information
Biological speciesErwinia amylovora (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsShanker, S. / Lawton, J.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The virulence-associated protein HsvA from the fire blight pathogen Erwinia amylovora is a polyamine amidinotransferase.
Authors: Shanker, S. / Schaefer, G.K. / Barnhart, B.K. / Wallace-Kneale, V.L. / Chang, D. / Coyle, T.J. / Metzler, D.A. / Huang, J. / Lawton, J.A.
History
DepositionAug 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HsvA
B: HsvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4345
Polymers90,2482
Non-polymers1863
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-21 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.543, 127.543, 92.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein HsvA


Mass: 45123.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia amylovora (bacteria) / Gene: hsvA / Production host: Escherichia coli (E. coli) / References: UniProt: Q58PW8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.4 Å3/Da / Density % sol: 48.74 % / Mosaicity: 0.9 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M MgCl2, 0.1 M HEPES pH 7.5, and 30% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→38.03 Å / Num. obs: 38767 / % possible obs: 100 % / Redundancy: 5.93 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 7.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.88 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
d*TREKdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.3→38.03 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.26
RfactorNum. reflection% reflection
Rfree0.226 1942 5.01 %
Rwork0.17 --
obs0.173 38762 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5953 0 12 282 6247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086157
X-RAY DIFFRACTIONf_angle_d0.8798371
X-RAY DIFFRACTIONf_dihedral_angle_d3.123652
X-RAY DIFFRACTIONf_chiral_restr0.053876
X-RAY DIFFRACTIONf_plane_restr0.0061088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.2841360.23312612X-RAY DIFFRACTION100
2.3575-2.42130.27541500.21832581X-RAY DIFFRACTION100
2.4213-2.49250.27941260.21572619X-RAY DIFFRACTION100
2.4925-2.57290.29661460.21372583X-RAY DIFFRACTION100
2.5729-2.66490.27591210.21572629X-RAY DIFFRACTION100
2.6649-2.77150.32161520.22242594X-RAY DIFFRACTION100
2.7715-2.89760.29141260.21732605X-RAY DIFFRACTION100
2.8976-3.05030.27341390.21922623X-RAY DIFFRACTION100
3.0503-3.24140.29171450.20422619X-RAY DIFFRACTION100
3.2414-3.49150.24991300.19282625X-RAY DIFFRACTION100
3.4915-3.84250.21081450.15362644X-RAY DIFFRACTION100
3.8425-4.39780.17381530.12582629X-RAY DIFFRACTION100
4.3978-5.53810.13891270.11812697X-RAY DIFFRACTION100
5.5381-38.03840.18461460.14362760X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8042-0.07380.36550.30110.1551.90080.0529-0.1235-0.08020.08520.051-0.04650.25220.0105-0.11260.28370.05750.00320.33910.03230.323748.204359.439433.0568
22.60841.52281.28652.12910.87272.79930.00470.1874-0.1530.02080.1261-0.32480.31350.5043-0.14750.27560.1120.00670.46920.00740.336158.799258.919317.3183
30.9753-0.18130.63590.4823-0.72291.9919-0.0113-0.01-0.00620.0287-0.0312-0.1080.14630.5130.05960.29930.10440.0020.4982-0.04350.362767.299860.040733.1776
40.5386-0.31290.19240.6354-0.28851.5247-0.0010.0181-0.0421-0.11730.04450.09190.0679-0.2111-0.06070.26290.0203-0.00630.3012-0.00740.298533.395471.133813.3928
51.60681.3733-0.33693.9642-1.01482.33680.0057-0.36850.16510.1844-0.05220.3892-0.1504-0.48150.00510.28650.10470.01630.4965-0.06150.313926.165177.366130.0038
60.6027-1.18270.74783.8977-0.46123.5059-0.0519-0.1744-0.05560.11510.18810.343-0.6498-0.5777-0.09210.33530.10530.01410.3983-0.01040.320832.043684.319427.2772
72.42620.09140.40322.710.30072.3676-0.0763-0.16480.14450.06660.07010.3471-0.4564-0.56370.03240.36920.15370.01220.40390.01690.356723.074589.541111.6214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 172 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 173 THROUGH 220 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 221 THROUGH 366 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 3 THROUGH 172 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 173 THROUGH 220 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 221 THROUGH 253 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 254 THROUGH 366 )

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