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- PDB-7u35: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate lig... -

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Basic information

Entry
Database: PDB / ID: 7u35
TitleCrystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with ADP
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 / ADP / 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 cycle / cell division / ATP binding / cytoplasm
Similarity search - Function
Mur ligase MurD-like, N-terminal domain / UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase, C-terminal / Mur ligase, 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
ADENOSINE-5'-DIPHOSPHATE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 in complex with ADP
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionFeb 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: 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
C: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4059
Polymers144,9373
Non-polymers1,4686
Water15,637868
1
A: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8023
Polymers48,3121
Non-polymers4892
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)48,8023
Polymers48,3121
Non-polymers4892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8023
Polymers48,3121
Non-polymers4892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.190, 131.180, 79.540
Angle α, β, γ (deg.)90.000, 106.931, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
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 10 and (name N...
d_3ens_1(chain "C" and (resid 8 through 16 or (resid 17...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISARGA1 - 32
d_12ens_1PROTHRA35 - 117
d_13ens_1LEUASPA119 - 165
d_14ens_1LEUILEA167 - 251
d_15ens_1GLYARGA253 - 295
d_16ens_1ARGVALA297 - 300
d_17ens_1TYRARGA302 - 346
d_18ens_1PROLEUA348 - 358
d_19ens_1GLYGLYA360
d_110ens_1ASPPROA362 - 375
d_111ens_1VALVALA377
d_112ens_1VALPHEA379 - 411
d_113ens_1ASNALAA413 - 429
d_114ens_1ADPADPB
d_115ens_1EDOEDOC
d_21ens_1HISARGD2 - 33
d_22ens_1PROTHRD36 - 118
d_23ens_1LEUASPD120 - 166
d_24ens_1LEUGLUD168 - 180
d_25ens_1HISILED188 - 259
d_26ens_1GLYARGD261 - 303
d_27ens_1ARGVALD305 - 308
d_28ens_1TYRARGD310 - 354
d_29ens_1PROLEUD356 - 366
d_210ens_1GLYGLYD368
d_211ens_1ASPPROD370 - 383
d_212ens_1VALVALD385
d_213ens_1VALPHED387 - 419
d_214ens_1ASNALAD421 - 437
d_215ens_1ADPADPE
d_216ens_1EDOEDOF
d_31ens_1HISTHRG1 - 115
d_32ens_1LEUASPG117 - 163
d_33ens_1LEUILEG165 - 249
d_34ens_1GLYARGG251 - 293
d_35ens_1ARGVALG295 - 298
d_36ens_1TYRARGG300 - 344
d_37ens_1PROLEUG346 - 356
d_38ens_1GLYGLYG358
d_39ens_1ASPPROG360 - 373
d_310ens_1VALVALG375
d_311ens_1VALPHEG377 - 409
d_312ens_1ASNALAG411 - 427
d_313ens_1ADPADPH
d_314ens_1EDOEDOI

NCS oper:
IDCodeMatrixVector
1given(0.997719455426, 0.0240425678347, 0.0630701450475), (-0.0527888333541, -0.304349731405, 0.951096514591), (0.0420621841743, -0.952256895972, -0.302386469169)38.6898280739, 11.950690659, 135.532196967
2given(0.993691269325, 0.0869560504966, -0.070825888971), (-0.00826574350581, -0.573024700319, -0.819496412627), (-0.111845155241, 0.814911859103, -0.568690885405)20.4788623392, 140.881106884, 42.5290292558

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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.: 3 / Fragment: PsaeA.17938.a.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / 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: 2.35 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.55
Details: Optimization condition around RigakuReagents JCSG Top96 B6: 21% (w/V) PEG 3350, 100mM HEPES/NaOH pH 7.55: PsaeA.17938.a.B2.PW38065 at 40mg/ml + 5mM ADP + 5mM MgCl2. Tray: 324078 e4: cryo: ...Details: Optimization condition around RigakuReagents JCSG Top96 B6: 21% (w/V) PEG 3350, 100mM HEPES/NaOH pH 7.55: PsaeA.17938.a.B2.PW38065 at 40mg/ml + 5mM ADP + 5mM MgCl2. Tray: 324078 e4: cryo: 20% EG + compounds in 2 steps: puck ECC9-7.

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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: Feb 17, 2022
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 95481 / % possible obs: 98.2 % / Redundancy: 5.111 % / Biso Wilson estimate: 37.332 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.049 / Χ2: 0.96 / Net I/σ(I): 21.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-24.7040.3144.2869200.9310.35396.4
2-2.065.1850.2555.7268270.9640.28397.3
2.06-2.125.2060.2097.1265710.9730.23297.4
2.12-2.185.1940.1688.8164510.9830.18797.9
2.18-2.255.2020.12911.2462750.9890.14397.8
2.25-2.335.1930.1113.1261000.9920.12298.1
2.33-2.425.1780.09415.1458560.9930.10498.1
2.42-2.525.2030.08317.1456760.9940.09298.2
2.52-2.635.1630.07219.354240.9960.0898.3
2.63-2.765.1670.062352080.9970.06798.7
2.76-2.915.1460.05326.1549420.9970.05998.6
2.91-3.085.130.04430.0847220.9980.04998.9
3.08-3.35.1050.03834.744300.9980.04399.1
3.3-3.565.0780.03538.2841230.9990.03999
3.56-3.95.0420.03240.9837900.9990.03699.1
3.9-4.365.0350.0343.434550.9990.03399.4
4.36-5.035.0450.02944.6730600.9990.03299.3
5.03-6.175.0380.02943.8925870.9990.03399
6.17-8.724.9790.02845.0920050.9990.03199.2
8.72-504.8230.02746.9110590.9990.0394.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20-4438refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure, pdb entry 7SY9, in two domains

7sy9


Resolution: 1.95→37.91 Å / SU ML: 0.1995 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3586
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 2000 2.09 %0
Rwork0.1705 93469 --
obs0.1713 95469 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.58 Å2
Refinement stepCycle: LAST / Resolution: 1.95→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9456 0 93 868 10417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00679799
X-RAY DIFFRACTIONf_angle_d0.849613344
X-RAY DIFFRACTIONf_chiral_restr0.05641569
X-RAY DIFFRACTIONf_plane_restr0.00741787
X-RAY DIFFRACTIONf_dihedral_angle_d11.26243526
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.15328917006
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.21093972772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.24361270.21056527X-RAY DIFFRACTION96.3
2-2.050.24671410.19916588X-RAY DIFFRACTION97.38
2.05-2.110.25261490.19156577X-RAY DIFFRACTION97.49
2.11-2.180.21721650.18126604X-RAY DIFFRACTION97.93
2.18-2.260.22821230.17536689X-RAY DIFFRACTION97.86
2.26-2.350.21341540.17496646X-RAY DIFFRACTION98.19
2.35-2.460.23571280.18196659X-RAY DIFFRACTION98.25
2.46-2.590.23391320.1866707X-RAY DIFFRACTION98.43
2.59-2.750.20461330.18496729X-RAY DIFFRACTION98.65
2.75-2.960.22291510.18686711X-RAY DIFFRACTION98.83
2.96-3.260.23851400.18016721X-RAY DIFFRACTION99.08
3.26-3.730.18251410.16596723X-RAY DIFFRACTION99.05
3.73-4.70.17171510.14526803X-RAY DIFFRACTION99.36
4.7-37.910.18791650.15876785X-RAY DIFFRACTION98.67
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)
12.30161806321-0.647437758391-0.6540130750438.38989463642-1.792931426662.622040805950.1080152162440.0264296870024-0.7940708549790.194705407832-0.450203808088-0.04531031287390.2229310903920.1170047715290.2865716757840.3663185022670.04258623277720.008288698112280.284527899045-0.04537146532950.600046235648-34.798505705744.989226335239.2071907017
22.22385512762-0.192820023531-0.04540950428522.584518476130.2282682671832.053433184610.1073662630570.02229018773430.00997493131307-0.205763483976-0.0445578310571-0.191627706696-0.2311334171630.114526530054-0.06270633761090.251575750381-0.01076655628150.02316005291960.1431975463960.02720037579720.150227063157-40.481108084372.899190176641.2228867597
31.29963250845-0.157953103060.463643616491.33612541066-0.09243221798923.132424662560.0135811925988-0.312647971404-0.00600641746533-0.0005111971116140.05647211242760.05443012272690.0255909417613-0.204508662028-0.07226100548140.134000193133-0.00915731033705-0.008563793596850.2115874485880.01709450098660.210374244435-48.097796518274.424521695163.4443641174
44.833446642161.137831270291.726330315745.16341005418-0.4906035298635.096180263960.254191398167-0.7569012289260.2761622419880.520883610793-0.113405751464-0.616415270135-0.7762213641190.12794683276-0.1371764254450.391541748349-0.09016992393760.02862426465750.396726150658-0.02669836406420.3297470044767.8787194074436.462974474580.4104942334
51.97135469575-0.4152081165630.08469395078252.12023576013-0.471070599143.525639228330.1197874869560.0514050121978-0.00274194576233-0.232531751340.001182739849580.04669092029240.2290025770280.0280718401738-0.1059625620440.3079913530030.0244028873286-0.005729837273040.1368262823940.00574012398250.1909819931840.25096061918932.743377850649.4072814873
62.283481531010.753318138213-0.5622896199113.05159055835-0.8829835840261.962244885570.06450722146320.0507466432890.330608420730.3437625324170.185890287620.65537716633-0.362554747449-0.244571074852-0.1740972010510.3841612667080.0899480504550.04802154412050.1906586484220.05290854664680.318664205531-2.09387030459.059418570442.6728557122
70.6918219821430.4991174394030.5500760998871.265693375840.05502485210510.638723220802-0.3765116051771.518718858981.2055661266-0.811740312227-0.138748013683-0.306770252816-0.6320719321031.273048500950.1714889657970.402404601082-0.442594318759-0.2263570849851.460676328930.7738013385851.02292284944-12.395515336284.098863125261.2878646507
82.506432712810.4714581860681.048034939033.32354286917-0.3476801406462.12979690397-0.08262230150520.2038724818990.3896801034720.116499482716-0.13335067177-0.114454418711-0.1684375211690.4065732827810.1188461310180.142890683177-0.025503247084-0.02219261438250.3929151547310.06665340675990.299996405974-15.38612739968.495307190180.0188884684
91.029352078450.1145867591270.0802666234713.063179455691.108045528061.942641951090.104336031712-0.0365261167778-0.003476268566520.262766091027-0.1887619518030.1649067207360.265483171177-0.2425794910640.07154918346880.170571769641-0.0135896451931-0.0006911747044950.3565397853780.03998975852590.233986548064-25.089949699450.926340826782.4838417191
103.1570511817-0.273401570783-0.8118858827534.829834067650.08191296842472.85497951040.008626588409290.68022073373-0.206785305953-0.742350541345-0.1826385233890.2669233622170.252916134081-0.4887527712560.1222078998660.3603406605980.0271923625448-0.06255284198020.462564687407-0.01084970199440.213935810087-24.675729678940.468626680764.8328573835
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 106 )AA8 - 1061 - 99
22chain 'A' and (resid 107 through 257 )AA107 - 257100 - 238
33chain 'A' and (resid 258 through 448 )AA258 - 448239 - 429
44chain 'B' and (resid 7 through 106 )BD7 - 1061 - 100
55chain 'B' and (resid 107 through 310 )BD107 - 310101 - 299
66chain 'B' and (resid 311 through 448 )BD311 - 448300 - 437
77chain 'C' and (resid 8 through 106 )CG8 - 1061 - 97
88chain 'C' and (resid 107 through 234 )CG107 - 23498 - 213
99chain 'C' and (resid 235 through 361 )CG235 - 361214 - 340
1010chain 'C' and (resid 362 through 448 )CG362 - 448341 - 427

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