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- PDB-8dof: Pseudomonas aeruginosa MurC with WYH9-2-P - OSA_001044 -

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Basic information

Entry
Database: PDB / ID: 8dof
TitlePseudomonas aeruginosa MurC with WYH9-2-P - OSA_001044
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / MurC / WYH9-2-P - OSA_001044 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


UDP-N-acetylmuramate-L-alanine ligase / UDP-N-acetylmuramate-L-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramate--L-alanine ligase / : / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
Chem-T4L / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHoranyi, P.S. / Wang, Y. / Todd, M.H. / Abendroth, J. / Edwards, T. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Pseudomonas aeruginosa MurC with WYH9-2-P - OSA_001044
Authors: Horanyi, P.S. / Wang, Y. / Todd, M.H. / Abendroth, J. / Edwards, T. / Lorimer, D.
History
DepositionJul 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8037
Polymers52,0401
Non-polymers7636
Water63135
1
A: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules

A: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,60614
Polymers104,0812
Non-polymers1,52612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/21
Buried area3090 Å2
ΔGint-57 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.210, 76.210, 132.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

21A-634-

HOH

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Components

#1: Protein UDP-N-acetylmuramate--L-alanine ligase / UDP-N-acetylmuramoyl-L-alanine synthetase


Mass: 52040.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: murC, PA4411 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HW02, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-T4L / (2R)-2-cyclohexyl-2-[(4-{[5-(propan-2-yl)-1H-pyrazol-3-yl]amino}-1H-pyrazolo[3,4-d]pyrimidin-6-yl)amino]ethan-1-ol


Mass: 384.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N8O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.85 Å3/Da / Density % sol: 33.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus II - A5; 30mM Lithium sulfate, 30mM Sodium sulfate, 30mM Potassium sulfate, 100mM 7.5 BES, Triethanolamine (TEA), 15% w/v PEG 3000, 20% v/v 1, 2, 4-Butanetriol, 1% w/v NDSB 256, 2mMcompound

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.6→38.25 Å / Num. obs: 12656 / % possible obs: 99.8 % / Redundancy: 11.75 % / Biso Wilson estimate: 54.9 Å2 / CC1/2: 0.994 / Net I/σ(I): 14.96
Reflection shellResolution: 2.6→2.67 Å / Num. unique obs: 910 / CC1/2: 0.989

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6x9n

6x9n


Resolution: 2.6→38.25 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1233 9.76 %
Rwork0.1876 11399 -
obs0.1926 12632 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.27 Å2 / Biso mean: 59.1475 Å2 / Biso min: 39.53 Å2
Refinement stepCycle: final / Resolution: 2.6→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 50 35 2293
Biso mean--64.91 55.24 -
Num. residues----301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.70.32071220.252712421364100
2.7-2.830.32371320.234812401372100
2.83-2.980.32881490.227312111360100
2.98-3.160.31431370.23512531390100
3.16-3.410.27691460.211512341380100
3.41-3.750.25211340.183612491383100
3.75-4.290.19811450.17112761421100
4.29-5.40.18821230.158713171440100
5.41-38.250.22061450.17581377152299
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)
15.92051.199136.5755-3.77318.66580.2377-0.1931-0.0736-0.21960.03180.86490.6394-1.0187-0.26430.366-0.04930.00030.5252-0.0990.4931-20.099523.7658-13.2399
28.5898-2.0046-2.54891.00881.67322.9644-0.0236-0.0975-0.0837-0.0439-0.05290.04540.1718-0.09740.05330.47180.04370.00710.271-0.00660.37830.546322.1876-14.9644
34.1476-1.51-0.00713.951-0.6724.38080.17580.1276-0.0299-0.1648-0.1725-0.08760.22620.2114-0.01330.36010.09580.03480.3539-0.03160.328415.702123.1533-21.517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 99 )A15 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 177 )A100 - 177
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 318 )A178 - 318

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