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- PDB-6nkj: 1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosam... -

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Basic information

Entry
Database: PDB / ID: 6nkj
Title1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with (2R)-2-(phosphonooxy)propanoic acid.
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / (2R)-2-(phosphonooxy)propanoic acid
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytoplasm
Similarity search - Function
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / : / 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
(2R)-2-(phosphonooxy)propanoic acid / CITRIC ACID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with (2R)-2-(phosphonooxy)propanoic acid.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2459
Polymers92,3882
Non-polymers8577
Water23,8161322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 3SG1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-13 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.713, 120.713, 70.614
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1 / Enoylpyruvate transferase 1 / UDP-N-acetylglucosamine enolpyruvyl transferase 1 / EPT 1


Mass: 46194.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: murA1, murA, SP_1966 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) MAGIC
References: UniProt: Q97NQ4, UDP-N-acetylglucosamine 1-carboxyvinyltransferase

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Non-polymers , 5 types, 1329 molecules

#2: Chemical ChemComp-0V5 / (2R)-2-(phosphonooxy)propanoic acid


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1322 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 11.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (B9), 1.8M Ammonium citrate pH=7.0; Cryo: 1.8M Ammonium citrate pH=7.0, 25% Sucrose.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 285243 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Rsym value: 0.049 / Χ2: 1.005 / Net I/σ(I): 22.2
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 14279 / CC1/2: 0.725 / Rpim(I) all: 0.378 / Rrim(I) all: 0.712 / Rsym value: 0.599 / Χ2: 1.005 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SG1

3sg1


Resolution: 1.3→27.77 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.404 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15494 13851 4.9 %RANDOM
Rwork0.14478 ---
obs0.14528 268642 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.3→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 52 1322 7710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137579
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177263
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.63710362
X-RAY DIFFRACTIONr_angle_other_deg0.4131.57716922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.47451039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.43122.822365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.512151399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5971548
X-RAY DIFFRACTIONr_chiral_restr0.0750.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0570.028922
X-RAY DIFFRACTIONr_gen_planes_other0.0550.021482
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9231.263904
X-RAY DIFFRACTIONr_mcbond_other0.921.2593903
X-RAY DIFFRACTIONr_mcangle_it1.4441.8915027
X-RAY DIFFRACTIONr_mcangle_other1.4441.8925028
X-RAY DIFFRACTIONr_scbond_it1.7851.5423675
X-RAY DIFFRACTIONr_scbond_other1.7791.543668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7612.2245336
X-RAY DIFFRACTIONr_long_range_B_refined5.47218.1118664
X-RAY DIFFRACTIONr_long_range_B_other4.96716.3988193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 1198 -
Rwork0.265 19688 -
obs--99.96 %
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)
11.2046-0.28360.03790.31010.05380.9516-0.0659-0.0855-0.12850.03040.00970.10110.0601-0.04480.05630.02860.00090.01320.01460.00740.037737.592324.693147.8593
20.8048-0.38450.14270.2829-0.0080.35640.02440.0599-0.0524-0.0029-0.02190.04770.013-0.0634-0.00260.00410.00020.00350.0344-0.0090.018535.068728.360617.3517
30.3397-0.0821-0.07990.10950.09530.61790.00820.02250.0102-0.008-0.0024-0.0076-0.03210.0583-0.00590.0058-0.00070.00330.0156-0.00090.003648.767733.718423.6125
40.5716-0.087-0.18890.23910.10490.4145-0.0189-0.0626-0.01210.02440.00830.0432-0.0169-0.03130.01060.00740.00860.00370.0385-0.00660.011638.434436.733646.7059
50.7943-0.51450.00240.7567-0.03810.90390.01780.0846-0.152-0.0377-0.07350.05620.0595-0.03430.05580.0153-0.0068-0.00030.0247-0.01510.03732.624244.861922.7075
60.5002-0.37680.01950.3722-0.1190.3469-0.039-0.0402-0.05980.03360.04210.01720.04930.0191-0.00310.03310.01570.0060.02570.00040.02917.49445.612854.0611
70.2779-0.1287-0.11140.1860.00390.6594-0.0003-0.01380.01340.0060.0059-0.0032-0.0714-0.0012-0.00560.01370.00410.00230.0063-0.00140.00293.980459.049545.2609
80.4215-0.1987-0.18860.37480.10440.43320.01640.0452-0.0428-0.0379-0.0276-0.00570.01770.02790.01120.02030.01710.00720.02160.0010.010412.612951.655223.8812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 152
3X-RAY DIFFRACTION3A153 - 266
4X-RAY DIFFRACTION4A267 - 421
5X-RAY DIFFRACTION5B1 - 23
6X-RAY DIFFRACTION6B24 - 161
7X-RAY DIFFRACTION7B162 - 266
8X-RAY DIFFRACTION8B267 - 421

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