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- PDB-3r38: 2.23 Angstrom resolution crystal structure of UDP-N-acetylglucosa... -

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Basic information

Entry
Database: PDB / ID: 3r38
Title2.23 Angstrom resolution crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) from Listeria monocytogenes EGD-e
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
KeywordsTRANSFERASE / Biosynthesis and Degradation of Murein Sacculus and Peptidoglycan / Infectious Diseases / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / 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
UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsHalavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.23 Angstrom resolution crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) from Listeria monocytogenes EGD-e
Authors: Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,76512
Polymers48,7691
Non-polymers99611
Water3,315184
1
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules

A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,53024
Polymers97,5382
Non-polymers1,99222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
2
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules

A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,53024
Polymers97,5382
Non-polymers1,99222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4660 Å2
ΔGint-274 kcal/mol
Surface area34560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.579, 51.923, 78.178
Angle α, β, γ (deg.)90.00, 110.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 48768.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo2526, murA, murA1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q8Y4C4, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 7.6 mg/mL protein in 10 mM Tris-HCl, 0.25 M sodium chloride, 5 mM BME. Crystallization condition: The Classics II Suite condition A5 (0.1 M HEPES, pH 7.5, 2 M ammonium sulfate). Cryo ...Details: 7.6 mg/mL protein in 10 mM Tris-HCl, 0.25 M sodium chloride, 5 mM BME. Crystallization condition: The Classics II Suite condition A5 (0.1 M HEPES, pH 7.5, 2 M ammonium sulfate). Cryo condition: 1:1 v/v 3.6 M ammonium sulfate : 50 % sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2011 / Details: Be-Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.23→30 Å / Num. all: 26370 / Num. obs: 26370 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.33
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.69 / Num. unique all: 1309 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RL2

2rl2


Resolution: 2.23→29.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.84 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23864 1328 5 %RANDOM
Rwork0.19627 ---
obs0.19841 25035 98.71 %-
all-25035 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.984 Å2
Baniso -1Baniso -2Baniso -3
1--3.86 Å2-0 Å2-0.73 Å2
2--0.08 Å20 Å2
3---3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.23→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 51 184 3518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223434
X-RAY DIFFRACTIONr_bond_other_d0.0010.022243
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9884662
X-RAY DIFFRACTIONr_angle_other_deg0.76935533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.965450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.70925.147136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.30715609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.7241519
X-RAY DIFFRACTIONr_chiral_restr0.0790.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023817
X-RAY DIFFRACTIONr_gen_planes_other00.02622
X-RAY DIFFRACTIONr_mcbond_it0.8181.52209
X-RAY DIFFRACTIONr_mcbond_other0.1991.5911
X-RAY DIFFRACTIONr_mcangle_it1.59723568
X-RAY DIFFRACTIONr_scbond_it2.92131225
X-RAY DIFFRACTIONr_scangle_it4.8064.51094
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 78 -
Rwork0.386 1553 -
obs-1553 83.38 %
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)
12.0744-0.667-0.08151.2838-0.57251.4860.00930.1927-0.4134-0.1161-0.1630.0344-0.00960.14270.15370.08740.0008-0.01870.0486-0.02940.109819.113328.08917.6274
21.8783-0.20350.25621.08550.30461.3987-0.0183-0.0403-0.0120.06250.0193-0.00160.0371-0.0763-0.00110.0479-0.01390.03410.0106-0.00650.05453.827236.308339.9335
31.9192-0.0422-0.02362.19580.27851.09550.06570.21440.064-0.1781-0.1592-0.06620.0370.04410.09350.1157-0.0046-0.01660.09980.03910.02617.428942.010813.1482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-9 - 24
2X-RAY DIFFRACTION2A25 - 231
3X-RAY DIFFRACTION3A232 - 430

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