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- PDB-7osq: Crystal structure of UDP-N-acetylenolpyruvoylglucosamine reductas... -

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Basic information

Entry
Database: PDB / ID: 7osq
TitleCrystal structure of UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) from Pseudomonas aeruginosa in complex with FAD and a pyrazole derivative (fragment 18)
ComponentsUDP-N-acetylenolpyruvoylglucosamine reductase
KeywordsOXIDOREDUCTASE / Peptidoglycan-biosynthesis / Fragment based drug discovery
Function / homology
Function and homology information


UDP-N-acetylmuramate dehydrogenase / UDP-N-acetylmuramate dehydrogenase activity / peptidoglycan biosynthetic process / FAD binding / cell wall organization / flavin adenine dinucleotide binding / regulation of cell shape / cell division / cytosol
Similarity search - Function
UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
Chem-0JI / FLAVIN-ADENINE DINUCLEOTIDE / UDP-N-acetylenolpyruvoylglucosamine reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsAcebron-Garcia de Eulate, M. / Mayol-Llinas, J. / Blundell, T.L. / Kim, S.Y. / Mendes, V. / Abell, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateCystic Fibrosis Trust United Kingdom
Citation
Journal: J.Med.Chem. / Year: 2022
Title: Discovery of Novel Inhibitors of Uridine Diphosphate- N -Acetylenolpyruvylglucosamine Reductase (MurB) from Pseudomonas aeruginosa , an Opportunistic Infectious Agent Causing Death in Cystic Fibrosis Patients.
Authors: Acebron-Garcia-de-Eulate, M. / Mayol-Llinas, J. / Holland, M.T.O. / Kim, S.Y. / Brown, K.P. / Marchetti, C. / Hess, J. / Di Pietro, O. / Mendes, V. / Abell, C. / Floto, R.A. / Coyne, A.G. / Blundell, T.L.
History
DepositionJun 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: 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-acetylenolpyruvoylglucosamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6683
Polymers37,6791
Non-polymers9892
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.651, 87.651, 101.148
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylmuramate dehydrogenase


Mass: 37678.863 Da / Num. of mol.: 1
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: murB, PA2977 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HZM7, UDP-N-acetylmuramate dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-0JI / 5-methyl-1-phenyl-1,2,3-triazole-4-carboxylic acid


Mass: 203.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 30% glycerol and 22% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.06693→75.908 Å / Num. obs: 27031 / % possible obs: 99.89 % / Redundancy: 20 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.5
Reflection shellResolution: 2.067→2.103 Å / Mean I/σ(I) obs: 1.5 / Num. measured obs: 27421 / Num. unique obs: 2183 / CC1/2: 0.352

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata processing
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JB1

4jb1


Resolution: 2.07→40.21 Å / SU ML: 0.2324 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 1272 4.71 %
Rwork0.2138 25723 -
obs0.2156 26995 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.4 Å2
Refinement stepCycle: LAST / Resolution: 2.07→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 68 79 2679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812653
X-RAY DIFFRACTIONf_angle_d1.27533617
X-RAY DIFFRACTIONf_chiral_restr0.0647404
X-RAY DIFFRACTIONf_plane_restr0.0065472
X-RAY DIFFRACTIONf_dihedral_angle_d27.1604379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.150.35141470.28412836X-RAY DIFFRACTION99.1
2.15-2.250.26261360.26812856X-RAY DIFFRACTION99.97
2.25-2.370.27061400.2532866X-RAY DIFFRACTION100
2.37-2.510.30751510.24112821X-RAY DIFFRACTION100
2.51-2.710.26291380.23272831X-RAY DIFFRACTION99.97
2.71-2.980.24871440.21922880X-RAY DIFFRACTION100
2.98-3.410.24921470.20562848X-RAY DIFFRACTION99.93
3.41-4.30.23861170.19042887X-RAY DIFFRACTION99.97
4.3-40.210.22671520.19152898X-RAY DIFFRACTION100
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)
11.831903716180.990842825138-0.9935953211733.6022891496-1.067509800344.03578504979-0.448555055219-0.0402652421847-0.399996987415-1.086274478740.350211601858-0.8429416574070.4813824646371.44569151550.07836971823330.553753223082-0.01372354784920.1937509235150.582573787253-0.137413547680.367538261455-26.52254770899.53934304624-15.2034320336
22.31785352840.775118061894-0.703401794764.047468322720.3898003212935.365193219720.0131152838881-0.2349196317690.05455539618720.05735804471850.159991768656-0.281499076592-0.2756737475561.19662156608-0.1500707213480.174524960798-0.05541286656390.002574535195410.338277884221-0.02542636792870.198796675119-32.174153335516.82682401145.02696668295
35.51615700152.16760052666-1.155535202382.10040263966-1.080364583034.02084288763-0.18211673680.5063028616440.320470573065-0.1025962912440.3811386125320.164963629916-1.000859351830.300936486693-0.1801506292920.491555669916-0.1295034567910.056848591330.2340161555720.03093210509010.32198906585-38.410142807624.761981972-7.13356249948
4-0.110752586928-0.2325599001460.7988208374512.283314186981.039032898182.176250529370.0264033091616-0.0470377537904-0.0219234650810.4179134871310.07638179886840.3540557224680.422819915693-0.307963251805-0.1492200953210.440300960483-0.1390773547150.004114226688490.435260983403-0.006040492152680.327771789208-39.959586953913.733637251314.5142167828
50.672280251214-0.0369264412833-1.750443444123.449521079811.816923522926.879381518880.255435981596-0.809896063889-0.0887962859960.234238048483-0.182964287758-0.6306783986342.412770079111.156099533640.09736773349160.6985214475970.2688423150630.0478728956747-0.158650785940.1394924599510.294987126513-38.9117682220.811613749888.2095173462
63.02871304445-0.423409124439-0.3015247103574.004645122251.324085698765.00651270412-0.141545969921-0.256497830179-0.3031419765550.847922126144-0.2389679642031.61051809371-0.275863925181-1.591436669940.2224883305850.4972582878070.08895668778780.15822798720.665419427598-0.04553370915870.707527273171-60.749040258510.923161651-1.04777527141
73.16389975092-0.173020260989-0.1194344374772.933728335360.7383310747894.11468147736-0.3474781860580.133479116076-0.238979883864-0.5209423689980.3587164078250.3060496283391.08475346644-0.6958289619380.0145507295150.664366205404-0.17615086147-0.0265415310030.221502856190.001218950671450.302832124532-51.06894917790.526908482293-9.48489938934
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 65 )3 - 651 - 63
22chain 'A' and (resid 66 through 147 )66 - 14764 - 145
33chain 'A' and (resid 148 through 176 )148 - 176146 - 174
44chain 'A' and (resid 177 through 212 )177 - 212175 - 210
55chain 'A' and (resid 213 through 237 )213 - 237211 - 235
66chain 'A' and (resid 238 through 270 )238 - 270236 - 268
77chain 'A' and (resid 271 through 339 )271 - 339269 - 337

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