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- PDB-6x9f: Pseudomonas aeruginosa MurC with AZ8074 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6x9f
TitlePseudomonas aeruginosa MurC with AZ8074
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / MurC / AZ8074 / 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-UXP / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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)
CitationJournal: To Be Published
Title: Pseudomonas aeruginosa MurC with AZ8074
Authors: Horanyi, P.S. / Mayclin, S.J. / Durand-Reville, T.F. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 2, 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)409,25066
Polymers403,2358
Non-polymers6,01458
Water10,557586
1
A: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1478
Polymers50,4041
Non-polymers7437
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)51,52213
Polymers50,4041
Non-polymers1,11712
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)51,0697
Polymers50,4041
Non-polymers6656
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)51,1999
Polymers50,4041
Non-polymers7948
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)51,1999
Polymers50,4041
Non-polymers7948
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)51,0597
Polymers50,4041
Non-polymers6546
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)50,9976
Polymers50,4041
Non-polymers5925
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)51,0597
Polymers50,4041
Non-polymers6546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)284.690, 109.050, 108.200
Angle α, β, γ (deg.)90.000, 112.260, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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 , 5 types, 644 molecules

#2: Chemical
ChemComp-UXP / [(2R)-1-{4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-2H-pyrazolo[3,4-d]pyrimidin-6-yl}piperidin-2-yl]methanol


Mass: 354.410 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H22N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 278 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: 2.35→47.67 Å / Num. obs: 126323 / % possible obs: 99 % / Redundancy: 3.216 % / Biso Wilson estimate: 48.651 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.077 / Χ2: 1.026 / Net I/σ(I): 11.42 / Num. measured all: 406260 / Scaling rejects: 17
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
2.35-2.413.2350.5842.0429938936792540.8280.70198.8
2.41-2.483.2380.4822.4629220912590230.8810.57998.9
2.48-2.553.2380.3992.9428699896288620.9110.47998.9
2.55-2.633.240.3153.6227700863985490.9440.37899
2.63-2.713.2270.2674.326815839983090.9560.32198.9
2.71-2.813.2370.2045.4725852806779870.9730.24599
2.81-2.913.2340.1656.5625148785477770.9810.19799
2.91-3.033.2220.1278.1124111755074830.990.15299.1
3.03-3.173.2280.1059.7623257726272050.9910.12699.2
3.17-3.323.2190.07612.7422074692768570.9950.09199
3.32-3.53.2060.06114.9320855656465040.9970.07399.1
3.5-3.723.2080.0517.619907625762060.9980.0699.2
3.72-3.973.20.04320.118543584257940.9980.05199.2
3.97-4.293.1960.03622.6717335546254240.9980.04499.3
4.29-4.73.2050.03225.0916179508050480.9980.03999.4
4.7-5.253.1940.03125.5614515457045440.9990.03899.4
5.25-6.073.1910.03423.4212778404440040.9990.04199
6.07-7.433.1640.03125.1310702341133820.9990.03799.1
7.43-10.513.1210.02430.998309267926620.9990.02999.4
10.51-47.672.9830.02431.814323152214490.9990.02995.2

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Processing

Software
NameVersionClassification
PHENIXPHENIX (dev_2733: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vvw

5vvw


Resolution: 2.35→47.67 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1999 1.59 %
Rwork0.1834 124105 -
obs0.184 126104 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.79 Å2 / Biso mean: 48.6931 Å2 / Biso min: 21.67 Å2
Refinement stepCycle: final / Resolution: 2.35→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17873 0 393 586 18852
Biso mean--66.81 50.41 -
Num. residues----2434
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 (%)
2.35-2.410.38861370.29158782891999
2.41-2.470.28791380.26838763890199
2.47-2.550.22941460.2438859900599
2.55-2.630.27811390.238840897999
2.63-2.720.2441440.21468821896599
2.72-2.830.2411440.20888807895199
2.83-2.960.2651410.2058868900999
2.96-3.120.2471430.20238884902799
3.12-3.310.26741390.19818871901099
3.31-3.570.2281490.198861901099
3.57-3.930.22531350.16578931906699
3.93-4.490.20451500.14189439093100
4.49-5.660.14181480.14918957910599
5.66-47.670.17571460.16838918906498
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)
19.01141.499-3.59588.07750.98337.65630.0868-0.0584-0.82570.3809-0.22850.40620.5402-0.46830.19730.3849-0.0439-0.09350.37760.13850.3895-32.9279.685-34.704
23.76120.8621-1.50072.6689-1.60794.829-0.0510.0287-0.1890.1198-0.10330.1199-0.1437-0.16140.16110.35290.0695-0.04160.35740.03840.2596-32.26921.757-45.803
33.0567-0.33330.15751.2746-0.00432.63-0.0390.30010.1080.0129-0.0271-0.1003-0.0156-0.0790.04880.40610.0167-0.07960.42420.1060.2648-32.31634.194-60.795
47.2447-3.6648-0.22328.6229-2.79356.4703-0.2798-1.0195-0.18050.67440.29240.04240.2654-0.15960.02510.3807-0.03320.00970.4389-0.05060.3249-37.63-23.33434.494
51.4859-0.84780.57275.7126-2.08932.5442-0.0914-0.09-0.05090.25960.1899-0.04790.11640.086-0.10330.3126-0.00790.03090.3466-0.1260.2918-30.268-12.36624.727
63.1498-0.12610.31183.8779-0.79221.77-0.07260.06740.01090.1901-0.0199-0.36770.0946-0.01620.0810.2764-0.072-0.00560.3211-0.09990.2723-15.448-3.42215.483
75.96390.17830.89874.3488-0.09322.8333-0.1627-0.18850.44730.21310.01260.0274-0.2242-0.23120.18320.2709-0.0677-0.01550.2716-0.04420.3053-28.0099.17314.886
82.40210.2849-3.38147.64060.43876.5551-0.0823-0.234-0.82510.34620.07980.42120.6931-0.3183-0.05370.4291-0.0294-0.11010.3657-0.01620.5044-52.264-44.8814.629
92.65520.0318-1.74951.6437-0.60613.3481-0.12760.1389-0.22430.00220.03990.1913-0.0509-0.27650.07310.3542-0.0317-0.05620.2931-0.07670.3024-51.338-32.734-6.601
104.3156-0.2869-0.75391.6233-0.48992.4659-0.09660.4153-0.00810.02-0.01540.03720.0815-0.27160.12730.3624-0.0202-0.10220.3609-0.06680.2329-51.423-20.24-21.331
115.0865-1.98180.30338.2466-0.87648.8271-0.0120.24490.6104-0.285-0.08740.0825-0.726-0.17310.09970.2705-0.0397-0.03140.3289-0.02330.4405-50.8563.6350.264
121.61260.5037-0.41842.6141-1.76215.4559-0.10380.0479-0.0691-0.09040.01110.1873-0.1519-0.22020.07350.2254-0.02740.03670.3053-0.08620.3116-57.871-8.5398.721
133.07010.53110.60071.44820.44234.199-0.0037-0.2254-0.1090.00030.008-0.1488-0.0624-0.3427-0.00680.23540.00430.0570.3897-0.0110.3967-68.405-21.09719.413
147.43583.005-1.28837.04180.28346.7289-0.02920.45530.0623-0.3738-0.0013-0.3039-0.14670.3099-0.02050.25520.0354-0.03470.2867-0.01740.2317-19.077-17.575-10.355
150.88071.322-0.72544.7965-1.69081.9073-0.080.05480.0048-0.01470.1288-0.0819-0.00320.1681-0.07120.3270.0262-0.0160.3407-0.10.2909-20.752-28.5951.934
162.64740.00750.58433.86510.09622.13490.03310.0338-0.0679-0.0578-0.0203-0.2369-0.0503-0.0275-0.03040.32310.0602-0.0040.2873-0.02860.2818-20.217-42.6915.45
177.0257-3.5273-0.57195.8103-1.87558.6995-0.1889-0.734-0.08620.31190.0238-0.0990.5695-0.16180.08930.36-0.14110.03090.40590.03750.3069-18.34631.041-4.746
181.8389-0.38440.236.0169-2.25152.6369-0.1418-0.14110.1015-0.01570.0763-0.14970.0341-0.00440.08330.2404-0.04730.04860.2475-0.02320.2509-10.72941.964-14.555
193.4219-0.68050.37983.503-0.16972.0704-0.10970.08090.25420.003-0.0215-0.06250.0479-0.14250.1440.3052-0.1049-0.00170.27730.06430.3233-0.96356.038-24.276
204.7243-1.03812.85996.8236-1.22888.68-0.15480.32850.7223-0.6006-0.15520.2896-0.8102-0.12950.26730.4151-0.0022-0.02420.36920.11030.5097-31.61658.132-39.058
211.44580.7975-1.06952.9346-2.02676.2043-0.03670.19710.1494-0.1777-0.01320.1875-0.1304-0.41540.06460.24810.00760.01220.35140.01010.3597-38.51146.067-30.533
222.35390.54470.18091.5827-0.18485.54160.0748-0.052-0.0282-0.0099-0.05230.0051-0.1872-0.37670.00920.2102-0.00380.05270.36640.03260.3674-49.0333.366-20.051
235.08643.071-1.44118.7981.18767.05020.10330.63690.3725-0.28580.1835-0.5381-0.49830.404-0.28910.41530.02130.01070.56630.19780.38890.17236.873-49.988
243.05531.3584-0.66255.2753-1.00851.74640.01490.0310.05440.02280.0861-0.0698-0.13380.1917-0.09080.31590.0286-0.01610.34920.07770.195-1.44125.85-37.663
252.17060.63570.79433.18040.2181.85190.03090.0674-0.04890.03260.065-0.14830.0087-0.0009-0.09750.27750.05650.00590.2980.10890.2495-0.75611.899-23.992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:81 )A8 - 81
2X-RAY DIFFRACTION2( CHAIN A AND RESID 82:170 )A82 - 170
3X-RAY DIFFRACTION3( CHAIN A AND RESID 171:311 )A171 - 311
4X-RAY DIFFRACTION4( CHAIN B AND RESID 8:81 )B8 - 81
5X-RAY DIFFRACTION5( CHAIN B AND RESID 82:170 )B82 - 170
6X-RAY DIFFRACTION6( CHAIN B AND RESID 171:257 )B171 - 257
7X-RAY DIFFRACTION7( CHAIN B AND RESID 258:311 )B258 - 311
8X-RAY DIFFRACTION8( CHAIN C AND RESID 8:81 )C8 - 81
9X-RAY DIFFRACTION9( CHAIN C AND RESID 82:170 )C82 - 170
10X-RAY DIFFRACTION10( CHAIN C AND RESID 171:312 )C171 - 312
11X-RAY DIFFRACTION11( CHAIN D AND RESID 8:81 )D8 - 81
12X-RAY DIFFRACTION12( CHAIN D AND RESID 82:170 )D82 - 170
13X-RAY DIFFRACTION13( CHAIN D AND RESID 171:311 )D171 - 311
14X-RAY DIFFRACTION14( CHAIN E AND RESID 8:81 )E8 - 81
15X-RAY DIFFRACTION15( CHAIN E AND RESID 82:170 )E82 - 170
16X-RAY DIFFRACTION16( CHAIN E AND RESID 171:311 )E171 - 311
17X-RAY DIFFRACTION17( CHAIN F AND RESID 8:81 )F8 - 81
18X-RAY DIFFRACTION18( CHAIN F AND RESID 82:170 )F82 - 170
19X-RAY DIFFRACTION19( CHAIN F AND RESID 171:312 )F171 - 312
20X-RAY DIFFRACTION20( CHAIN G AND RESID 8:81 )G8 - 81
21X-RAY DIFFRACTION21( CHAIN G AND RESID 82:170 )G82 - 170
22X-RAY DIFFRACTION22( CHAIN G AND RESID 171:311 )G171 - 311
23X-RAY DIFFRACTION23( CHAIN H AND RESID 8:81 )H8 - 81
24X-RAY DIFFRACTION24( CHAIN H AND RESID 82:170 )H82 - 170
25X-RAY DIFFRACTION25( CHAIN H AND RESID 171:311 )H171 - 311

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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

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