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- PDB-3sg1: 2.6 Angstrom Crystal Structure of UDP-N-acetylglucosamine 1-carbo... -

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Basic information

Entry
Database: PDB / ID: 3sg1
Title2.6 Angstrom Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1 (MurA1) from Bacillus anthracis
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Cell wall formation
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
TRIETHYLENE GLYCOL / UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMinasov, G. / Halavaty, A. / Filippova, E.V. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.6 Angstrom Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1 (MurA1) from Bacillus anthracis.
Authors: Minasov, G. / Halavaty, A. / Filippova, E.V. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,6396
Polymers198,2954
Non-polymers3442
Water8,899494
1
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1


Theoretical massNumber of molelcules
Total (without water)49,5741
Polymers49,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9183
Polymers49,5741
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1


Theoretical massNumber of molelcules
Total (without water)49,5741
Polymers49,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1


Theoretical massNumber of molelcules
Total (without water)49,5741
Polymers49,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-14 kcal/mol
Surface area54420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.666, 125.217, 79.472
Angle α, β, γ (deg.)90.00, 105.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 1 - 419 / Label seq-ID: 25 - 443

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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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: 49573.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS5137, BA_5529, GBAA_5529, murA1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS
References: UniProt: Q81K13, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 1.9 Å3/Da / Density % sol: 35.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein solution: 7.7 mg/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3), Screen solution: PEG's II, condition D10, 0.2M Sodium acetate, 0.1M Tris (pH 8.5), 30% (w/v) PEG 4000, VAPOR ...Details: Protein solution: 7.7 mg/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3), Screen solution: PEG's II, condition D10, 0.2M Sodium acetate, 0.1M Tris (pH 8.5), 30% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 45804 / Num. obs: 45804 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 12.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2277 / % 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: 1EJD

1ejd


Resolution: 2.6→29.88 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.884 / SU B: 27.754 / SU ML: 0.268 / Isotropic thermal model: Individually Refined / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25472 2299 5 %RANDOM
Rwork0.1798 ---
all0.1836 43242 --
obs0.1836 43242 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.778 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0 Å20.45 Å2
2---0.02 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12624 0 23 494 13141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02212934
X-RAY DIFFRACTIONr_bond_other_d0.0010.028784
X-RAY DIFFRACTIONr_angle_refined_deg1.271.97617464
X-RAY DIFFRACTIONr_angle_other_deg0.772321530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.61251695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.4724.473541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.892152331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3421595
X-RAY DIFFRACTIONr_chiral_restr0.0730.22031
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114509
X-RAY DIFFRACTIONr_gen_planes_other00.022434
X-RAY DIFFRACTIONr_mcbond_it1.021.58349
X-RAY DIFFRACTIONr_mcbond_other0.3121.53476
X-RAY DIFFRACTIONr_mcangle_it1.937213394
X-RAY DIFFRACTIONr_scbond_it3.29634585
X-RAY DIFFRACTIONr_scangle_it5.5064.54070
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5103 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.620.5
Bmedium positional0.560.5
Cmedium positional0.530.5
Dmedium positional0.560.5
Amedium thermal0.462
Bmedium thermal0.492
Cmedium thermal0.462
Dmedium thermal0.452
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 160 -
Rwork0.249 3169 -
obs-3169 99.91 %
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)
13.57030.4734-0.02912.52810.14052.4723-0.01590.1130.11470.04270.17060.0826-0.26040.0419-0.15470.0946-0.03010.0320.1086-0.00380.034420.132929.82712.3923
21.32570.0144-0.03771.8899-0.58662.37050.05110.0254-0.08430.07290.115-0.03440.16460.0733-0.16610.09020.0403-0.04160.0486-0.05660.111721.26992.268912.8784
32.6115-0.13730.08242.06320.26452.15360.05750.0688-0.1194-0.06680.0493-0.0130.1718-0.0279-0.10680.0424-0.0162-0.00250.03090.01510.035514.602423.680142.3679
42.4202-0.36980.52721.93-0.08142.2937-0.02240.14490.0201-0.10520.0152-0.0187-0.18750.09490.00710.0539-0.02140.01140.0162-0.00330.00419.751.15932.6317
52.8355-0.04290.37431.48720.0522.9458-0.12510.09090.1291-0.2340.0361-0.04010.0562-0.0610.0890.1006-0.0015-0.00190.03390.05470.1214-14.389147.391415.7637
63.4049-0.06260.061.7388-0.66351.7267-0.0035-0.33190.0077-0.0104-0.0076-0.02830.06260.04560.01110.03040.04440.01020.15290.01130.0222-21.436236.710342.4078
73.63960.05940.26581.59410.78982.1775-0.0365-0.2889-0.01870.166-0.0898-0.0410.0913-0.10650.12630.167-0.0291-0.00290.08480.06010.0817-15.78367.356520.5241
81.83630.0922-0.11362.0932-0.73843.080.0816-0.00720.1241-0.0033-0.1494-0.0144-0.10850.21430.06790.02520.00590.00270.04670.01460.0154-15.361718.1768-7.0374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION1A232 - 419
3X-RAY DIFFRACTION2A20 - 231
4X-RAY DIFFRACTION3B1 - 19
5X-RAY DIFFRACTION3B232 - 419
6X-RAY DIFFRACTION4B20 - 231
7X-RAY DIFFRACTION5C1 - 19
8X-RAY DIFFRACTION5C232 - 419
9X-RAY DIFFRACTION6C20 - 231
10X-RAY DIFFRACTION7D1 - 19
11X-RAY DIFFRACTION7D232 - 419
12X-RAY DIFFRACTION8D20 - 231

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