[English] 日本語
Yorodumi
- PDB-6wfm: Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransf... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more