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- PDB-7sy9: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate lig... -

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Basic information

Entry
Database: PDB / ID: 7sy9
TitleCrystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1
ComponentsUDP-N-acetylmuramoylalanine--D-glutamate ligase
KeywordsLIGASE / SSGCID / UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase / MurD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal 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
ACETATE ION / FORMIC ACID / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / 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)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1
Authors: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: 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

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylmuramoylalanine--D-glutamate ligase
B: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7765
Polymers96,6252
Non-polymers1513
Water95553
1
A: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4173
Polymers48,3121
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3582
Polymers48,3121
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.750, 94.750, 442.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 8 through 10 and (name N...
d_2ens_1(chain "B" and (resid 8 through 94 or (resid 95...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISTHRA1 - 31
d_12ens_1PROVALA35 - 48
d_13ens_1ARGCYSA51 - 61
d_14ens_1ARGVALA64 - 177
d_15ens_1GLYALAA179 - 433
d_21ens_1HISALAD1 - 425

NCS oper: (Code: givenMatrix: (-0.854372654473, 0.154632996511, -0.496120956702), (-0.293762503805, 0.643805256439, 0.706553878441), (0.428661823174, 0.749402047083, -0.504624229681)Vector: -27. ...NCS oper: (Code: given
Matrix: (-0.854372654473, 0.154632996511, -0.496120956702), (-0.293762503805, 0.643805256439, 0.706553878441), (0.428661823174, 0.749402047083, -0.504624229681)
Vector: -27.0457680001, -60.4395686245, 63.7653750466)

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Components

#1: Protein UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase


Mass: 48312.270 Da / Num. of mol.: 2 / Fragment: PsaeA.17938.a.B2
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: murD, PA4414 / Plasmid: PsaeA.17938.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HVZ9, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular dimensions/Calibre Morpheus screen, condition G6: 10% (w/V) PEG 8000, 20% (V/V) ethylene glycol: 20mM of each sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, ...Details: Molecular dimensions/Calibre Morpheus screen, condition G6: 10% (w/V) PEG 8000, 20% (V/V) ethylene glycol: 20mM of each sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, potassium sodium tartrate tetrahydrate, sodium oxamate: 100mM Sodium HEPES: MOPS (acid) pH 7.5: PsaeA.17938.a.B2.PS38064 at 46mg/ml: tray 320910 g6: cryo: direct: puck hdj1-6.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2021
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 31984 / % possible obs: 99.7 % / Redundancy: 10.538 % / Biso Wilson estimate: 74.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.072 / Χ2: 0.958 / Net I/σ(I): 20.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.75-2.8211.4860.6013.5622940.9370.629100
2.82-2.911.2780.4934.3722370.9470.516100
2.9-2.9811.2530.3745.6322050.9780.392100
2.98-3.0711.6470.297.5221120.9830.303100
3.07-3.1811.3440.2219.6320840.990.232100
3.18-3.2911.1110.17912.3419960.9920.18799.9
3.29-3.4110.7870.14115.8119460.9940.148100
3.41-3.5511.0570.11620.0418440.9960.122100
3.55-3.7110.4740.10222.3418160.9960.108100
3.71-3.8910.8970.08327.3217170.9970.08799.8
3.89-4.110.230.07231.2216680.9980.07699.8
4.1-4.359.4140.06432.4315590.9980.06899.7
4.35-4.659.4880.05734.9514690.9980.0699.5
4.65-5.029.2910.05535.9214030.9990.05999.9
5.02-5.59.7770.05635.9212960.9980.05999.8
5.5-6.159.560.05136.3411740.9990.05499.8
6.15-7.19.2420.04737.1610590.9990.04999.2
7.1-8.79.2850.0440.369190.9990.04298.8
8.7-12.38.790.03441.677370.9990.03697.5
12.3-508.2810.02540.244910.02790.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20rc3 4406refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 5a5f in two domains as per Morda

5a5f


Resolution: 2.75→47.38 Å / SU ML: 0.3961 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 2021 6.34 %0
Rwork0.2119 29878 --
obs0.2141 31899 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.4 Å2
Refinement stepCycle: LAST / Resolution: 2.75→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6173 0 10 53 6236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00446277
X-RAY DIFFRACTIONf_angle_d0.71798534
X-RAY DIFFRACTIONf_chiral_restr0.04761010
X-RAY DIFFRACTIONf_plane_restr0.00631126
X-RAY DIFFRACTIONf_dihedral_angle_d12.51272169
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.25244498897 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.30471480.26282075X-RAY DIFFRACTION99.96
2.82-2.890.26551260.26142074X-RAY DIFFRACTION100
2.9-2.980.39271330.3062104X-RAY DIFFRACTION99.96
2.98-3.080.32521590.30422050X-RAY DIFFRACTION100
3.08-3.190.34721400.26732100X-RAY DIFFRACTION99.96
3.19-3.310.28591440.2382082X-RAY DIFFRACTION99.96
3.31-3.460.24211440.23792096X-RAY DIFFRACTION100
3.46-3.650.28661440.24922141X-RAY DIFFRACTION100
3.65-3.880.31541410.23692093X-RAY DIFFRACTION100
3.88-4.170.2061540.1952135X-RAY DIFFRACTION99.91
4.18-4.590.21551440.16752135X-RAY DIFFRACTION99.56
4.59-5.260.19191540.17872179X-RAY DIFFRACTION99.79
5.26-6.620.22411230.20772228X-RAY DIFFRACTION99.79
6.62-47.380.22981670.1872386X-RAY DIFFRACTION99.03
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)
12.554696957830.3400887135891.387746548791.16417380632-0.7686435625615.645382970260.2037172317640.1440047628040.0467636862393-0.712086128127-0.3026298319740.336868605169-0.253921559449-0.3627311568470.1130105579980.8503511957450.206370175066-0.1671015508820.62643598946-0.0981919584680.55810835568-48.960682784444.420519983438.6922479384
23.776745678560.819703472071-2.338608836621.41611682883-0.8526944968192.31754469321-0.0515839843222-0.0946711769672-0.06126993163160.164793095009-0.1552355885610.19331363598-0.0788155494465-0.2464915265250.2037940697410.4403784355950.0158927197013-0.009058847362160.735026742189-0.1441082110350.421956336732-53.577557403934.70636399368.3264373128
34.263811227940.3699863604940.6125600529994.261156902342.5971396152.646099488430.1731440542690.6376587163072.086115959830.4922602988090.612383764192-0.57407050630.6659265022990.290975591189-0.741365099970.852180578627-0.0394397782752-0.4034178131640.9098939220450.09333558390381.991435650599.503993121159.0391255423260.0169812817
42.57165115981.10995152752.251234590226.35490954608-4.147967221157.63587236380.2198179666420.908493397231-2.03482380459-1.00851533408-0.695447286695-2.632539626340.3018143181871.752809861330.1011873264930.8898710876730.182192397573-0.284059840981.62909071345-0.7053887311172.6749358504917.294853724.0284220666857.1429574364
55.29442000501-1.800516431091.657611782851.58183431075-0.2383569906923.77268924580.991341964061-0.298504927836-1.27399625350.514250498488-0.979097855842-1.824587204021.2550877989-0.0763078814693-0.2211257374631.08982528937-0.212515276564-0.4309780532190.9035939168680.2173176166452.028716987632.80728007516-3.3370342883159.654058303
63.78407019615-1.496042176881.07156986484.95142966036-1.928735834652.977698680410.0984224182598-0.381686955385-0.8253339068240.386658440442-0.0377037264606-2.1423688111-0.2421208761990.407864819186-0.04606543388970.611201774104-0.208060019985-0.1849568970980.6664904289250.1641251915511.22029506299-3.9588629246319.65320010354.3372655073
74.076578795240.4544614672622.157373930153.549631031740.4017785370534.129926446170.334953304795-1.06909467945-0.871486445660.613972291155-0.416729429186-0.967259193980.6579517038920.02634931419110.05009451214560.682189101877-0.237769308706-0.1057100310010.8369846731080.3111774658320.890198922722-12.4659843168.8180903561652.7294371435
87.8211182422-5.239137029443.428417568889.41729498659-2.161866686574.384426203260.666813977406-0.870367584608-1.111917473920.422770482562-0.3410034704431.107707459670.0677343891483-0.521457303342-0.4147914274220.638995952635-0.1826191786430.03116819854170.742363496640.07271437344780.598448191678-22.896226514216.87501078751.3307791127
92.347403728431.25785217954-2.123079826171.03885641345-0.2893548150578.42706219415-0.02987842788390.0260290553799-0.0332010608596-0.087403667098-0.12331734657-0.352106461417-0.3655055251550.2409796095730.1165320230820.477259804646-0.02422722261750.05565084355620.3976299826060.08953547259220.49546659398-12.266672477129.420096301534.8701573476
102.95629777586-1.022922590531.874052152437.43886251587-0.4685514442536.351495052440.01946016072790.70552624384-0.580539823828-0.93758977287-0.189256865999-0.2760424397460.6047789007890.710531677930.1788460232230.7504638941990.01910645825520.3096378871410.5940213063860.09524393221820.622658193195-4.0680134927323.548269700412.6912043298
113.353301620671.62997109760.7726266970942.569483732010.06891981919285.0707476784-0.438335559975-0.320535376921-0.2004417371040.05124236558120.238225318882-0.6344173415-0.4888176993361.079230857840.2196454957520.608479857789-0.1004389292650.1829116062050.814896458140.1567096163660.697142124242.4728689209531.620629372323.3791944824
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 195 )AA8 - 1951 - 180
22chain 'A' and (resid 196 through 448 )AA196 - 448181 - 433
33chain 'B' and (resid 8 through 29 )BD8 - 291 - 22
44chain 'B' and (resid 30 through 63 )BD30 - 6323 - 51
55chain 'B' and (resid 64 through 98 )BD64 - 9852 - 84
66chain 'B' and (resid 99 through 169 )BD99 - 16985 - 155
77chain 'B' and (resid 170 through 205 )BD170 - 205156 - 182
88chain 'B' and (resid 206 through 243 )BD206 - 243183 - 220
99chain 'B' and (resid 244 through 360 )BD244 - 360221 - 337
1010chain 'B' and (resid 361 through 400 )BD361 - 400338 - 377
1111chain 'B' and (resid 401 through 448 )BD401 - 448378 - 425

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