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- PDB-8egn: Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (UDP-N... -

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Basic information

Entry
Database: PDB / ID: 8egn
TitleCrystal Structure of UDP-N-acetylmuramate-L-alanine ligase (UDP-N-acetylmuramoyl-L-alanine synthetase, MurC) Pseudomonas aeruginosa in complex with ligand AZ-13643701
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / SSGCID / murC / UDP-N-acetylmuramoyl-L-alanine synthetase / Cell wall biogenesis / peptidoglycan biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 cycle / 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 family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
Chem-WIR / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle 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)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (UDP-N-acetylmuramoyl-L-alanine synthetase, MurC) Pseudomonas aeruginosa in complex with ligand AZ-13643701
Authors: Abendroth, J. / Dranow, D.M. / Hill, P. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation_author
Revision 1.2Oct 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,9826
Polymers67,9532
Non-polymers1,0294
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-38 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.690, 75.160, 109.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 5 and (name N or name...
d_2ens_1(chain "B" and (resid 5 through 29 or resid 31...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISLEUA3 - 27
d_12ens_1LEUVALA29 - 71
d_13ens_1SERPROA73 - 94
d_14ens_1ALAALAA96 - 125
d_15ens_1VALALAA127 - 146
d_16ens_1GLNALAA149 - 158
d_17ens_1ALAASPA160 - 183
d_18ens_1ASPPROA191 - 231
d_19ens_1VALTHRA233 - 258
d_110ens_1LEUASPA260 - 291
d_111ens_1GLYVALA293 - 309
d_112ens_1701701B
d_113ens_1SO4SO4C
d_21ens_1HISLEUD1 - 25
d_22ens_1LEUVALD27 - 69
d_23ens_1SERPROD71 - 92
d_24ens_1ALAALAD94 - 123
d_25ens_1VALALAD125 - 144
d_26ens_1GLNALAD146 - 155
d_27ens_1ALAPROD157 - 221
d_28ens_1VALTHRD223 - 248
d_29ens_1LEUASPD250 - 281
d_210ens_1GLYVALD283 - 299
d_211ens_1701701E
d_212ens_1SO4SO4F

NCS oper: (Code: givenMatrix: (-0.869702402953, 0.473871361018, 0.1380712262), (0.465417930409, 0.694211689762, 0.549050343641), (0.164328574361, 0.541771227554, -0.824305802869)Vector: -18. ...NCS oper: (Code: given
Matrix: (-0.869702402953, 0.473871361018, 0.1380712262), (0.465417930409, 0.694211689762, 0.549050343641), (0.164328574361, 0.541771227554, -0.824305802869)
Vector: -18.8192402309, -10.5129874054, 48.7701369697)

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Components

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


Mass: 33976.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: murC, PA4411 / Plasmid: PsaeA.00137.b.B5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HW02, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical ChemComp-WIR / (1R,2S)-1-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl)amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2,3-dihydro-1H-inden-2-ol


Mass: 418.495 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: Molecular Dimensions Morpheus II, optimization screen around condition A1 and A10: 100mM Bis-Tris/HCl pH 6.6, 13% (w/V) PEG 3000, 18%(V/V) 1,2,4-butanetriol, 30mM lithum sulfate, 30mM ...Details: Molecular Dimensions Morpheus II, optimization screen around condition A1 and A10: 100mM Bis-Tris/HCl pH 6.6, 13% (w/V) PEG 3000, 18%(V/V) 1,2,4-butanetriol, 30mM lithum sulfate, 30mM potassium sulfate: PseaA.00137.b.B5.PW37941 + 1mM BSI111802/AZ13643701: tray: 325364 b5: cryo: direct: puck fkc8-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1807 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 18, 2022
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1807 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 43967 / % possible obs: 100 % / Redundancy: 6.386 % / Biso Wilson estimate: 42.572 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.048 / Χ2: 0.915 / Net I/σ(I): 21.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-26.0280.6182.6132190.8520.677100
2-2.066.6940.4823.5931200.9230.523100
2.06-2.126.5670.3674.7330520.9520.399100
2.12-2.186.4370.2855.8629440.9660.31100
2.18-2.256.630.2357.2428810.9790.255100
2.25-2.336.4150.1789.2627700.9880.194100
2.33-2.426.7150.14411.5726910.9920.157100
2.42-2.526.5320.11713.8725950.9960.128100
2.52-2.636.4130.09916.2624580.9960.108100
2.63-2.766.5290.07620.924010.9970.083100
2.76-2.916.3940.0626.4322770.9980.065100
2.91-3.086.550.04932.4621310.9990.053100
3.08-3.36.210.03938.1520330.9990.04299.9
3.3-3.566.4180.03245.6319040.9990.03599.9
3.56-3.96.1420.02850.5217350.9990.03199.9
3.9-4.366.2140.02656.4515940.9990.02999.9
4.36-5.035.8810.02457.3414310.9990.02799.9
5.03-6.175.9590.02656.2712060.9990.02899.9
6.17-8.725.7970.02357.989640.9990.026100
8.72-505.4010.0260.6156110.02398.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1 4694refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 6X9N as per MoRDa, MurC same crystal form

6x9n


Resolution: 1.95→37.7 Å / SU ML: 0.2162 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3059
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 2003 4.56 %0
Rwork0.1794 41949 --
obs0.1812 43952 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.07 Å2
Refinement stepCycle: LAST / Resolution: 1.95→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 72 281 4840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00694690
X-RAY DIFFRACTIONf_angle_d0.87836406
X-RAY DIFFRACTIONf_chiral_restr0.0576750
X-RAY DIFFRACTIONf_plane_restr0.0074836
X-RAY DIFFRACTIONf_dihedral_angle_d12.39241657
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.78900693949 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.26661820.24722928X-RAY DIFFRACTION99.94
2-2.050.2941600.22112944X-RAY DIFFRACTION99.97
2.05-2.110.25171510.20982928X-RAY DIFFRACTION99.94
2.11-2.180.25921360.20272955X-RAY DIFFRACTION100
2.18-2.260.25461370.20332987X-RAY DIFFRACTION100
2.26-2.350.2351490.19742948X-RAY DIFFRACTION99.94
2.35-2.460.24911500.18842945X-RAY DIFFRACTION99.94
2.46-2.590.26281250.19523005X-RAY DIFFRACTION99.97
2.59-2.750.21981330.19782992X-RAY DIFFRACTION100
2.75-2.960.2771150.20543034X-RAY DIFFRACTION99.97
2.96-3.260.22271540.19133000X-RAY DIFFRACTION99.9
3.26-3.730.21941350.1753009X-RAY DIFFRACTION99.94
3.73-4.70.18291280.14553075X-RAY DIFFRACTION99.88
4.7-37.70.18341480.16533199X-RAY DIFFRACTION99.88
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)
15.652093538051.237893900381.478155398981.759987395860.8457755549774.963142076860.0915635339397-0.02316319185080.2066327577970.1861203294240.0199394385790.0681368654973-0.0498195104449-0.134969405656-0.1119607927740.281257970140.03716155403290.002495345013430.208989193535-0.01072104334910.22535497501-2.67823893161-1.1191792366848.266458268
22.91117739445-0.523583208502-0.534464441371.73953163227-0.1009663634813.929204598030.0142857378417-0.195345768348-0.27318014246-0.0146862240725-0.01900602142380.03395148046260.1496270257670.170323545602-0.02042102950040.213875375232-0.02471396615830.005596378461510.209587925850.04818388302240.26451037501111.8698963241-1.5054519520820.2752767089
33.45463996756-0.743828547321-0.2818923448723.608904167131.021228280496.49233459462-0.01754663694090.2739509424940.276694353507-0.2071675471610.008552175501840.209494371661-0.5272368885970.184172420170.01340875214640.404797169253-0.110016246634-0.02625483907770.2909937707650.03913044111090.370286729124-11.613138092715.91697575676.55544546539
42.06616807704-0.272595654624-2.56560181860.1186558568740.7227128543175.031878025770.1014077387620.06778083008250.0876380111435-0.1433602153720.04119875064090.0233945894756-0.187805502581-0.142352925123-0.1558302132030.295558011886-0.0351769737326-0.04232528031530.2611989259770.02701122231480.304241203369-18.042661330510.902265936119.7952716785
53.05702711323-0.20175955898-1.020998563122.85720278733-0.4760395836472.94884369787-0.04257679479480.0498226101783-0.260248498712-0.170746717158-0.04666629618050.02138866190080.347942103085-0.1239633997770.1221555151860.284910947284-0.0711637366595-0.04455391503080.246045673962-0.02799355665790.239405405256-23.9294926481-1.1445786438533.57986553
64.537023505161.18407551921-2.385563293297.67766475311.08162677294.08093130858-0.0616958723951-0.07984241580730.1590204593010.04769448104110.1009877413970.567109571277-0.268003875208-0.453629433189-0.01928132167530.2102979870430.0276543454228-0.01589305922740.3159248865850.03531108415210.262341972364-33.711583231811.899409671238.9834697441
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 107 )AA3 - 1071 - 105
22chain 'A' and (resid 108 through 313 )AA108 - 313106 - 309
33chain 'B' and (resid 5 through 81 )BD5 - 811 - 77
44chain 'B' and (resid 82 through 158 )BD82 - 15878 - 151
55chain 'B' and (resid 159 through 257 )BD159 - 257152 - 243
66chain 'B' and (resid 258 through 313 )BD258 - 313244 - 299

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