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- PDB-6x9n: Pseudomonas aeruginosa MurC with AZ5595 -

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Basic information

Entry
Database: PDB / ID: 6x9n
TitlePseudomonas aeruginosa MurC with AZ5595
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / MurC / PsaeA.00137.b / AZ5595 / 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 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-UYD / VALINE / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHoranyi, P.S. / Mayclin, S.J. / Durand-Reville, T.F. / Lorimer, D.D. / Edwards, T.E. / 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 AZ5595
Authors: Horanyi, P.S. / Mayclin, S.J. / Durand-Reville, T.F. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: UDP-N-acetylmuramate--L-alanine ligase
D: UDP-N-acetylmuramate--L-alanine ligase
E: UDP-N-acetylmuramate--L-alanine ligase
F: UDP-N-acetylmuramate--L-alanine ligase
G: UDP-N-acetylmuramate--L-alanine ligase
H: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)410,09273
Polymers403,2358
Non-polymers6,85765
Water15,853880
1
A: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1738
Polymers50,4041
Non-polymers7687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,59314
Polymers50,4041
Non-polymers1,18913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1738
Polymers50,4041
Non-polymers7687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2519
Polymers50,4041
Non-polymers8468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2519
Polymers50,4041
Non-polymers8468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,31310
Polymers50,4041
Non-polymers9099
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1117
Polymers50,4041
Non-polymers7066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2288
Polymers50,4041
Non-polymers8237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)285.650, 109.100, 108.430
Angle α, β, γ (deg.)90.000, 112.280, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 50404.387 Da / Num. of mol.: 8
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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9HW02, UDP-N-acetylmuramate-L-alanine ligase

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Non-polymers , 6 types, 945 molecules

#2: Chemical
ChemComp-UYD / (2R)-2-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl)amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2-phenylethan-1-ol


Mass: 406.484 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H26N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-VAL / VALINE / Valine


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus A2, 60mM Divalents, (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate), 100mM Imidazole; MES monohydrate (acid), 20% v/v Ethylene glycol; 10 % w/v PEG 8000. 1mM ...Details: Morpheus A2, 60mM Divalents, (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate), 100mM Imidazole; MES monohydrate (acid), 20% v/v Ethylene glycol; 10 % w/v PEG 8000. 1mM compound was soaked over 4 days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→47.748 Å / Num. obs: 145819 / % possible obs: 99.8 % / Redundancy: 4.262 % / Biso Wilson estimate: 37.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.083 / Χ2: 1.027 / Net I/σ(I): 11.41 / Num. measured all: 621465 / Scaling rejects: 32
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
2.25-2.314.2740.5572.64598210779107580.90.63799.8
2.31-2.374.290.4733.14480510466104450.9150.54199.8
2.37-2.444.2870.3953.584367710208101880.9450.45299.8
2.44-2.524.2890.3344.242466992199000.9590.38199.8
2.52-2.64.290.2744.9441254963396160.9720.31399.8
2.6-2.694.2930.222639713926792500.9790.25499.8
2.69-2.794.2890.1757.2538513899789800.9870.299.8
2.79-2.94.2880.1428.8336870861785990.990.16299.8
2.9-3.034.2830.11210.435461828882800.9940.12899.9
3.03-3.184.2740.09412.3633985796779520.9950.10899.8
3.18-3.354.2650.07415.131959750674930.9960.08499.8
3.35-3.564.2410.06217.2130496720871900.9970.07199.8
3.56-3.84.240.05319.4628298668466740.9980.06199.9
3.8-4.114.2330.04721.5826410625262390.9980.05499.8
4.11-4.54.2270.04223.7824535581758040.9980.04899.8
4.5-5.034.2220.0424.6921951521151990.9980.04699.8
5.03-5.814.2070.04223.2219351461146000.9980.04899.8
5.81-7.124.1870.04323.1316383392639130.9980.04999.7
7.12-10.064.160.03627.4812745307630640.9980.04299.6
10.06-47.7483.9470.03528.136611172616750.9980.0497

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Processing

Software
NameVersionClassification
PHENIX(dev_2744: ???)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vvw

5vvw


Resolution: 2.25→47.748 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 2002 1.37 %
Rwork0.1813 143618 -
obs0.1818 145620 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.25 Å2 / Biso mean: 44.4557 Å2 / Biso min: 22.41 Å2
Refinement stepCycle: final / Resolution: 2.25→47.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17913 0 447 880 19240
Biso mean--53.11 49.95 -
Num. residues----2439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818810
X-RAY DIFFRACTIONf_angle_d0.86225585
X-RAY DIFFRACTIONf_chiral_restr0.0552984
X-RAY DIFFRACTIONf_plane_restr0.0053340
X-RAY DIFFRACTIONf_dihedral_angle_d7.46114744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.30620.29151380.255910224100
2.3062-2.36860.2821490.246710177100
2.3686-2.43830.31071410.239610234100
2.4383-2.5170.32181460.227910228100
2.517-2.60690.25011460.213810226100
2.6069-2.71130.24961410.200610209100
2.7113-2.83470.20131390.189910240100
2.8347-2.98410.22121380.188210239100
2.9841-3.1710.25371430.191710264100
3.171-3.41580.23121430.182910296100
3.4158-3.75940.21021480.174310293100
3.7594-4.30310.18191370.149710270100
4.3031-5.42020.19891410.149910393100
5.4202-47.7480.19331520.17411032599
Refinement TLS params.Method: refined / Origin x: -30.3374 Å / Origin y: 1.9229 Å / Origin z: -12.4387 Å
111213212223313233
T0.2881 Å2-0.0015 Å2-0.0176 Å2-0.3145 Å2-0.0145 Å2--0.2526 Å2
L0.155 °20.0126 °20.0034 °2-0.1774 °2-0.0758 °2--0.1697 °2
S0.0272 Å °0.0295 Å °0.0154 Å °-0.0151 Å °-0.0237 Å °0.0213 Å °0.0174 Å °-0.0559 Å °-0.0039 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allS1 - 674
2X-RAY DIFFRACTION1allS675 - 892
3X-RAY DIFFRACTION1allA15 - 508
4X-RAY DIFFRACTION1allB15 - 319
5X-RAY DIFFRACTION1allB508
6X-RAY DIFFRACTION1allC15 - 319
7X-RAY DIFFRACTION1allC508
8X-RAY DIFFRACTION1allD15 - 319
9X-RAY DIFFRACTION1allD508
10X-RAY DIFFRACTION1allE15 - 319
11X-RAY DIFFRACTION1allE508
12X-RAY DIFFRACTION1allF15 - 319
13X-RAY DIFFRACTION1allF508
14X-RAY DIFFRACTION1allG15 - 319
15X-RAY DIFFRACTION1allG508
16X-RAY DIFFRACTION1allH15 - 319
17X-RAY DIFFRACTION1allH320 - 508
18X-RAY DIFFRACTION1allI1 - 37
19X-RAY DIFFRACTION1allJ1 - 30
20X-RAY DIFFRACTION1allJ31
21X-RAY DIFFRACTION1allK1 - 8

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