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- PDB-4ziy: Structure of UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopim... -

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Basic information

Entry
Database: PDB / ID: 4ziy
TitleStructure of UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase from Acinetobacter baumannii
ComponentsUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
KeywordsLIGASE / SSGCID / Acinetobacter baumannii / UDP-N-acetylmuramoylalanyl-D-glutamyl-2 / 6-diaminopimelate--D-alanyl-D-alanyl ligase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-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-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain ...UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, 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 / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
Similarity search - Component
Biological speciesAcinetobacter baumannii AB5075 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase from Acinetobacter baumannii
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Clifton, M.C. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6006
Polymers51,8841
Non-polymers7175
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.090, 86.090, 131.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase


Mass: 51883.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria)
Strain: AB5075-UW / Gene: murF, A591_A0258 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0A2TK68, UniProt: A0A0D5YEC3*PLUS, UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MCSG1 screen G4: 20% PEG 3350, 200mM Na-tartrate; AcbaC.00137.c.B1.PS02364 at 22.7mg/ml with 3mM MgCl2 and AMPPNP; Cryo: 20% EG + compounds; tray: 262682g4; puck rrn3-1; iodide data set was ...Details: MCSG1 screen G4: 20% PEG 3350, 200mM Na-tartrate; AcbaC.00137.c.B1.PS02364 at 22.7mg/ml with 3mM MgCl2 and AMPPNP; Cryo: 20% EG + compounds; tray: 262682g4; puck rrn3-1; iodide data set was prepared by soaking a crystal from the same well in reservoir with 10%EG and 250mM NaI, and 20% EG and 500mM NaI

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
SYNCHROTRONAPS 21-ID-G20.97856
Detector
TypeIDDetectorDate
RIGAKU SATURN 944+1CCDApr 17, 2015
RAYONIX MX-3002CCDApr 17, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2[111]
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.978561
ReflectionNumber: 227924 / Rmerge(I) obs: 0.088 / Χ2: 1.1 / D res high: 2.45 Å / Num. obs: 39759 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
10.965043610.027
7.7510.9681410.028
6.337.75106510.041
5.486.33123810.056
4.95.48142710.052
4.474.9154210.045
4.144.47171010.049
3.874.14183110.053
3.653.87194510.063
3.463.65204110.07
3.33.46216310.085
3.163.3229210.108
3.043.16233610.134
2.933.04249110.161
2.832.93250010.206
2.742.83260410.24
2.662.74274610.291
2.582.66277710.324
2.512.58284110.361
2.452.51296010.428
ReflectionResolution: 1.85→50 Å / Num. all: 48643 / Num. obs: 48617 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 34.238 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.058 / Χ2: 0.999 / Net I/σ(I): 21.45 / Num. measured all: 359513
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.85-1.97.50.9280.5313.526494354635460.571100
1.9-1.950.960.3794.8725830346734660.408100
1.95-2.010.9750.2866.3425220337533750.307100
2.01-2.070.9870.2168.1824556328232820.232100
2.07-2.140.9910.17210.223553314431440.185100
2.14-2.210.9930.13712.4823221310131010.147100
2.21-2.290.9960.10815.4222072294529450.115100
2.29-2.390.9960.116.8721581288428840.107100
2.39-2.490.9970.0820.6620383272527250.086100
2.49-2.620.9980.06923.919863265626550.074100
2.62-2.760.9980.0626.5318579249524950.064100
2.76-2.930.9980.05430.2617689238223820.058100
2.93-3.130.9990.04635.0316636224322430.05100
3.13-3.380.9990.04139.1715335208820880.044100
3.38-3.70.9990.03643.4914027192319230.039100
3.7-4.140.9990.03546.412895178617840.03899.9
4.14-4.780.9990.03448.0611253156715660.03699.9
4.78-5.850.9990.03447.159441133713360.03799.9
5.85-8.270.9990.03347.037297106310630.035100
8.27-500.9980.03344.5435886346140.03696.8

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
ARP3.15model building
Cootmodel building
PHENIX(dev_2006: ???)refinement
PDB_EXTRACTdata extraction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→37.682 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 2486 5.12 %Random selection
Rwork0.1734 ---
obs0.1749 48541 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.07 Å2 / Biso mean: 47.4615 Å2 / Biso min: 17.77 Å2
Refinement stepCycle: final / Resolution: 1.85→37.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 44 315 3689
Biso mean--38.8 45.16 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083490
X-RAY DIFFRACTIONf_angle_d0.9664747
X-RAY DIFFRACTIONf_chiral_restr0.051549
X-RAY DIFFRACTIONf_plane_restr0.005632
X-RAY DIFFRACTIONf_dihedral_angle_d13.1191264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8501-1.88570.26491190.260125472666100
1.8857-1.92420.26661350.2325172652100
1.9242-1.9660.28191380.211925402678100
1.966-2.01170.22131280.196425322660100
2.0117-2.0620.21911340.186725252659100
2.062-2.11780.21961340.186225292663100
2.1178-2.18010.23731500.17925042654100
2.1801-2.25040.22151260.177625502676100
2.2504-2.33090.22151350.175325702705100
2.3309-2.42420.22321090.172625512660100
2.4242-2.53450.19881560.176125512707100
2.5345-2.66810.20461700.181924892659100
2.6681-2.83520.21231420.178225592701100
2.8352-3.0540.21411310.182425892720100
3.054-3.36120.22751520.177325622714100
3.3612-3.84710.19311360.15625852721100
3.8471-4.84530.14231510.138826292780100
4.8453-37.68960.20081400.18532726286699
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)
16.76950.2123-0.24942.35550.35134.5460.0812-0.1209-0.2703-0.091-0.0868-0.15050.156-0.0115-0.00340.1844-0.019-0.01670.10450.01460.1936-9.523720.542627.3327
21.24380.7479-0.75641.2256-0.93371.84860.0692-0.00940.06310.0330.02630.0306-0.046-0.1214-0.08510.15760.02930.01480.182-0.0120.16433.393241.905618.1102
31.9087-0.07570.20281.3294-0.60872.57530.06720.25960.1229-0.04070.21120.30880.0901-0.7568-0.20890.2359-0.03010.01930.42540.08030.22520.808347.09480.6461
43.3023-0.7932-1.12072.46090.613.49790.1587-0.28610.62870.3984-0.10750.7907-0.3147-1.4465-0.0550.68290.03250.24231.38630.11590.8431-21.584356.98461.7798
52-4.327422-2.2881.99990.09160.1235-0.02150.9164-0.0503-0.69390.84380.7586-0.03670.909-0.42470.03231.3327-0.32291.6242-27.631941.6333-7.1031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 80 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 277 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 346 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 347 through 463 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 464 through 465 )A0

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