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- PDB-7tm4: Crystal structure of apo 3-phosphoshikimate 1-carboxyvinyltransfe... -

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Basic information

Entry
Database: PDB / ID: 7tm4
TitleCrystal structure of apo 3-phosphoshikimate 1-carboxyvinyltransferase from Klebsiella pneumoniae
Components3-phosphoshikimate 1-carboxyvinyltransferase
KeywordsTRANSFERASE / 3-phosphoshikimate 1-carboxyvinyltransferase / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm
Similarity search - Function
EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / 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) ...EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / 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
NITRATE ION / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To be published
Title: Crystal structure of apo 3-phosphoshikimate 1-carboxyvinyltransferase from Klebsiella pneumoniae
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C.
History
DepositionJan 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1782
Polymers47,1161
Non-polymers621
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.709, 43.709, 171.067
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein 3-phosphoshikimate 1-carboxyvinyltransferase / 5-enolpyruvylshikimate-3-phosphate synthase / EPSP synthase / EPSPS


Mass: 47115.641 Da / Num. of mol.: 1 / Fragment: KlpnC.18288.a.B1
Source method: isolated from a genetically manipulated source
Details: Cocrystallized with shikimate-3-phosphate. However, the ligand was not observed in the active site and may have been displaced by the high halogen anion concentrations in the crystallization solution.
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: aroA, KPHS_18160 / Plasmid: KlpnC.18288.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3GV01, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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 Å3/Da / Density % sol: 38.57 % / Mosaicity: 0.14 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus B8: 9.375 (v/v) 2-methyl-2,4-pentanediol: 9.375 (v/v) PEG 1000: 9.375 (v/v) PEG 3350, 0.1M (Sodium HEPES: MOPS), 0.03 M Sodium fluoride: 0.03 M Sodium bromide: 0.03 M Sodium iodide) ...Details: Morpheus B8: 9.375 (v/v) 2-methyl-2,4-pentanediol: 9.375 (v/v) PEG 1000: 9.375 (v/v) PEG 3350, 0.1M (Sodium HEPES: MOPS), 0.03 M Sodium fluoride: 0.03 M Sodium bromide: 0.03 M Sodium iodide), KlpnC.18288.a.B1.PW39049 at 20 mg/mL, Tray: plate 12156 well B8 drop 1, Puck: PSL0615, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.46
ReflectionResolution: 1.7→85.53 Å / Num. obs: 40195 / % possible obs: 99.8 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.029 / Rrim(I) all: 0.064 / Net I/σ(I): 15.8 / Num. measured all: 200342 / Scaling rejects: 6
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
1.7-1.735.20.6831103621380.630.3370.7632.3100
9-85.535.40.02615002780.9990.0120.02943.699.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G6T

1g6t


Resolution: 1.7→57.02 Å / Cross valid method: THROUGHOUT / σ(F): 31.08 / Phase error: 23.77 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2126 2117 5.28 %
Rwork0.182 38009 -
obs0.2027 40126 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.44 Å2 / Biso mean: 24.749 Å2 / Biso min: 14.77 Å2
Refinement stepCycle: final / Resolution: 1.7→57.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 4 86 3273
Biso mean--20.35 23.02 -
Num. residues----426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083251
X-RAY DIFFRACTIONf_angle_d1.1284423
X-RAY DIFFRACTIONf_dihedral_angle_d6.402465
X-RAY DIFFRACTIONf_chiral_restr0.066525
X-RAY DIFFRACTIONf_plane_restr0.013578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.740.39611040.34032591269596
1.74-1.780.36761400.30332485262595
1.78-1.830.29281620.29652584274694
1.83-1.890.30051320.27262505263795
1.89-1.950.25231320.25332545267795
1.95-2.020.2671300.24592537266795
2.02-2.10.24711540.22342576273094
2.1-2.190.22891580.2272506266494
2.19-2.310.26311770.21742525270293
2.31-2.450.2921300.21942516264695
2.45-2.640.2507900.21712559264997
2.64-2.910.24441500.21032572272294
2.91-3.330.28121080.19542537264595
3.33-4.190.20581640.17222465262993
4.19-57.020.19061860.14372506269293
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)
11.80010.012-0.17160.8766-0.40012.52630.0839-0.06730.062-0.0464-0.05110.00580.0565-0.0713-0.03390.1998-0.0233-0.00240.1884-0.00180.162311.20617.13714.29
21.4751-0.00470.10230.7049-0.16760.37250.0032-0.0383-0.0207-0.0077-0.01620.0062-0.0079-0.02070.0140.14270.0295-0.00350.179-0.00240.1388-1.2758.444-12.729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:19 OR RESID 241:427 ) )A2 - 19
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:19 OR RESID 241:427 ) )A241 - 427
3X-RAY DIFFRACTION2( CHAIN A AND RESID 20:240 )A20 - 240

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