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- PDB-6wfm: Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransf... -

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Basic information

Entry
Database: PDB / ID: 6wfm
TitleCrystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) from Stenotrophomonas maltophilia K279a
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsTRANSFERASE / SSGCID / Stenotrophomonas maltophilia / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / murA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) from Stenotrophomonas maltophilia K279a
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
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

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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
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase


Theoretical massNumber of molelcules
Total (without water)91,1352
Polymers91,1352
Non-polymers00
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-4 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.740, 136.950, 155.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 3 or resid 5...
21(chain B and (resid 0 through 3 or resid 5...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISLYSLYS(chain A and (resid 0 through 3 or resid 5...AA0 - 38 - 11
12VALVALGLYGLY(chain A and (resid 0 through 3 or resid 5...AA5 - 1413 - 22
13GLUGLUGLUGLU(chain A and (resid 0 through 3 or resid 5...AA1523
14HISHISPROPRO(chain A and (resid 0 through 3 or resid 5...AA0 - 4238 - 431
15HISHISPROPRO(chain A and (resid 0 through 3 or resid 5...AA0 - 4238 - 431
16HISHISPROPRO(chain A and (resid 0 through 3 or resid 5...AA0 - 4238 - 431
17HISHISPROPRO(chain A and (resid 0 through 3 or resid 5...AA0 - 4238 - 431
21HISHISLYSLYS(chain B and (resid 0 through 3 or resid 5...BB0 - 38 - 11
22VALVALVALVAL(chain B and (resid 0 through 3 or resid 5...BB5 - 1613 - 24
23HISHISHISHIS(chain B and (resid 0 through 3 or resid 5...BB08
24HISHISHISHIS(chain B and (resid 0 through 3 or resid 5...BB08
25HISHISHISHIS(chain B and (resid 0 through 3 or resid 5...BB4856
26HISHISPROPRO(chain B and (resid 0 through 3 or resid 5...BB0 - 4238 - 431
27HISHISPROPRO(chain B and (resid 0 through 3 or resid 5...BB0 - 4238 - 431
28HISHISPROPRO(chain B and (resid 0 through 3 or resid 5...BB0 - 4238 - 431
29HISHISPROPRO(chain B and (resid 0 through 3 or resid 5...BB0 - 4238 - 431

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Components

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


Mass: 45567.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: murA, Smlt1119
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: B2FRX1, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic MCSG-1 screen, condition g7: 25% (w/V) PEG 3350, 100mM Tris base / HCl pH 8.5: StmaA.00952.a.B1.PW38746 (labelled as StmaA.01067.a.B1.PW38746) at 9mg/ml: tray 314074g7: cryo: 15% ...Details: Microlytic MCSG-1 screen, condition g7: 25% (w/V) PEG 3350, 100mM Tris base / HCl pH 8.5: StmaA.00952.a.B1.PW38746 (labelled as StmaA.01067.a.B1.PW38746) at 9mg/ml: tray 314074g7: cryo: 15% EG: puck qvy9-5. For phasing, a crystal from the same condition was incubated for 20sec in a mix of 90% reservoir and 10% 2.5M NaI in EG, followed by a soak for 20sec in a mix of 80% reservoir and 20% NaI in EG. cryo: 20% EG + 500mM NaI: puck ynn3-13

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDFeb 13, 2020
RIGAKU SATURN 944+2CCDFeb 17, 2020
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1C111SINGLE WAVELENGTHMx-ray1
2RIGAKU VARIMAX VHFSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.54181
ReflectionResolution: 1.95→37.23 Å / Num. obs: 66158 / % possible obs: 99.8 % / Redundancy: 6.176 % / Biso Wilson estimate: 44.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.056 / Χ2: 1.034 / Net I/σ(I): 18.03 / Num. measured all: 408609
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.95-26.2610.5952.6130351485048480.9170.649100
2-2.066.2580.4373.4829701474947460.9490.47799.9
2.06-2.126.2330.2945.0628746461346120.980.321100
2.12-2.186.2680.2366.2727874445044470.9850.25799.9
2.18-2.256.2620.1917.7527146433543350.9890.208100
2.25-2.336.2720.1529.5426205418141780.9930.16599.9
2.33-2.426.280.12611.6525497406240600.9940.137100
2.42-2.526.2520.10214.2624452391639110.9960.11199.9
2.52-2.636.2760.08417.1623579376137570.9970.09299.9
2.63-2.766.2130.0720.8422223358135770.9980.07699.9
2.76-2.916.2020.06224.4621160341634120.9980.06899.9
2.91-3.086.1670.05327.8819974324932390.9980.05899.7
3.08-3.36.1030.04931.6518480303530280.9980.05399.8
3.3-3.566.0260.04434.6417126285128420.9990.04899.7
3.56-3.960.04136.8315834264326390.9980.04599.8
3.9-4.365.9910.03938.5914252238623790.9990.04299.7
4.36-5.035.9720.03639.2512714213421290.9990.0499.8
5.03-6.175.9620.03539.1410737180118010.9990.038100
6.17-8.725.9020.03439.318411142714250.9990.03799.9
8.72-37.235.230.03537.6241478287930.9980.03995.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18rc4refinement
PDB_EXTRACT3.25data extraction
SHELXDEphasing
SHELXEmodel building
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→37.23 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 2019 3.05 %0
Rwork0.1709 ---
obs0.1722 66100 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.74 Å2 / Biso mean: 49.1715 Å2 / Biso min: 25.23 Å2
Refinement stepCycle: final / Resolution: 1.95→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6067 0 0 476 6543
Biso mean---49.75 -
Num. residues----833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076203
X-RAY DIFFRACTIONf_angle_d0.8358457
X-RAY DIFFRACTIONf_chiral_restr0.0551056
X-RAY DIFFRACTIONf_plane_restr0.0051100
X-RAY DIFFRACTIONf_dihedral_angle_d20.9592254
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3570X-RAY DIFFRACTION7.836TORSIONAL
12B3570X-RAY DIFFRACTION7.836TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.3431440.261245294673100
2-2.050.29931460.241244954641100
2.05-2.110.22991550.210345574712100
2.11-2.180.25091460.199145234669100
2.18-2.260.25061450.198745444689100
2.26-2.350.23931470.197345464693100
2.35-2.460.25161410.195445404681100
2.46-2.590.25041470.191245624709100
2.59-2.750.26161400.184945614701100
2.75-2.960.2531400.191845914731100
2.96-3.260.22961510.181345714722100
3.26-3.730.20921590.162845924751100
3.73-4.70.1711230.142946734796100
4.7-37.230.18291350.14864797493299
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)
15.0129-2.19511.39371.0247-0.69611.7827-0.1484-0.0673-0.20280.01360.07650.11730.0111-0.20070.07740.3949-0.07690.06130.3213-0.02950.2806-13.234-34.310227.071
21.5391-0.18210.52063.1622-0.28334.2925-0.24540.26350.25220.03930.1313-0.0121-0.8581-0.06810.13050.4241-0.0259-0.0950.4849-0.03360.3318-20.189-18.632715.724
32.1391-0.82570.70992.3099-0.17612.2439-0.15910.43380.2056-0.0273-0.04810.1368-0.2551-0.07050.21940.3852-0.094-0.09190.5698-0.00070.3503-19.8932-22.98455.0528
42.7489-0.86690.51061.2249-0.34571.3789-0.04880.2951-0.5123-0.09570.01260.19250.3599-0.15450.00240.3828-0.0860.05760.3134-0.09410.302-6.1884-44.094914.013
52.86160.1743-0.79850.66660.62325.0240.08350.15170.2008-0.06030.0375-0.0867-0.17080.2195-0.1040.353-0.00190.08320.2556-0.03220.308311.2328-35.224122.9816
66.686-3.4810.79441.8373-0.63841.4415-0.3431-0.05810.4390.16740.1569-0.3321-0.23780.18320.19890.4044-0.1129-0.03170.3299-0.0120.430416.9005-1.363833.7928
72.7819-1.15720.14062.83910.74991.64940.02130.7616-0.1064-0.2335-0.0569-0.22140.06910.19990.03740.3074-0.09790.10740.64070.0280.538830.4455-14.752222.1979
82.4818-0.57410.68970.9551-0.14951.32790.03270.58130.9914-0.1574-0.1753-0.4769-0.5730.3980.02550.5601-0.13290.07360.45350.20560.638616.73268.261319.2883
93.20760.016-0.40931.233-0.35244.75780.17870.49220.101-0.3016-0.0666-0.0060.0749-0.1748-0.06260.39880.0201-0.04480.29790.07280.3093-3.3702-0.195619.8613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 80 )A0 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 139 )A81 - 139
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 194 )A140 - 194
4X-RAY DIFFRACTION4chain 'A' and (resid 195 through 309 )A195 - 309
5X-RAY DIFFRACTION5chain 'A' and (resid 310 through 423 )A310 - 423
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 80 )B0 - 80
7X-RAY DIFFRACTION7chain 'B' and (resid 81 through 194 )B81 - 194
8X-RAY DIFFRACTION8chain 'B' and (resid 195 through 309 )B195 - 309
9X-RAY DIFFRACTION9chain 'B' and (resid 310 through 423 )B310 - 423

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