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- PDB-3i12: The crystal structure of the D-alanyl-alanine synthetase A from S... -

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Basic information

Entry
Database: PDB / ID: 3i12
TitleThe crystal structure of the D-alanyl-alanine synthetase A from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
ComponentsD-alanine-D-alanine ligase A
KeywordsLIGASE / D-alanyl-alanine synthetase A / ADP binding protein / CSGID / ATP-binding / Cell shape / Cell wall biogenesis/degradation / Magnesium / Manganese / Metal-binding / Nucleotide-binding / Peptidoglycan synthesis / Structural Genomics / NIAID Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosol
Similarity search - Function
D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain ...D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / D-alanine--D-alanine ligase A
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R. / Maltseva, N. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of the D-alanyl-alanine synthetase A from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Authors: Zhang, R. / Maltseva, N. / Papazisi, L. / Anderson, W. / Joachimiak, A.
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-alanine-D-alanine ligase A
B: D-alanine-D-alanine ligase A
C: D-alanine-D-alanine ligase A
D: D-alanine-D-alanine ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,2918
Polymers157,5824
Non-polymers1,7094
Water5,675315
1
A: D-alanine-D-alanine ligase A
B: D-alanine-D-alanine ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6464
Polymers78,7912
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-30 kcal/mol
Surface area27490 Å2
MethodPISA
2
C: D-alanine-D-alanine ligase A
D: D-alanine-D-alanine ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6464
Polymers78,7912
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-31 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.153, 85.813, 230.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
D-alanine-D-alanine ligase A / D-alanylalanine synthetase A / D-Ala-D-Ala ligase A


Mass: 39395.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2' / Gene: ddlA, STM0380 / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A1F0, D-alanine-D-alanine ligase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 2.2→115.47 Å / Num. all: 82180 / Num. obs: 82073 / % possible obs: 99.87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 29.56
Reflection shellResolution: 2.2→2.259 Å / Redundancy: 9 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 2.34 / Num. unique all: 6236 / % possible all: 98.76

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→47.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.774 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.241 / ESU R Free: 0.206
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24918 4332 5 %RANDOM
Rwork0.19697 ---
obs0.1996 82073 99.87 %-
all-82180 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.034 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10681 0 108 315 11104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02211020
X-RAY DIFFRACTIONr_bond_other_d0.0010.027161
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.96715000
X-RAY DIFFRACTIONr_angle_other_deg1.097317605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2551407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50925.316491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.166151806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2421556
X-RAY DIFFRACTIONr_chiral_restr0.1280.21755
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022053
X-RAY DIFFRACTIONr_mcbond_it1.0521.57020
X-RAY DIFFRACTIONr_mcbond_other0.2471.52867
X-RAY DIFFRACTIONr_mcangle_it1.927211295
X-RAY DIFFRACTIONr_scbond_it3.10134000
X-RAY DIFFRACTIONr_scangle_it4.9114.53705
LS refinement shellResolution: 2.2→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 323 -
Rwork0.22 5909 -
obs-6232 98.76 %
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)
10.41120.1618-0.13290.7188-0.68230.8869-0.0270.0204-0.0227-0.03490.06640.05230.1236-0.0519-0.03940.1059-0.00640.05270.0156-0.00040.053544.05626.36649.037
21.20440.02410.1340.2018-0.21370.411-0.05630.11170.15590.00590.04550.01560.00870.05570.01090.0653-0.01390.04220.07490.00040.064462.95943.51736.681
30.54070.1603-0.23390.3529-0.07480.8511-0.03920.0313-0.0761-0.0399-0.07640.07170.1385-0.03860.11550.03780.01070.02670.0469-0.02390.078792.24834.4492.564
40.84940.4847-0.25870.5663-0.19120.40120.02760.01610.13460.0266-0.07260.03440.01860.05790.0450.00660.01380.01350.08450.05230.1119108.53357.3575.625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 100
2X-RAY DIFFRACTION1A101 - 200
3X-RAY DIFFRACTION1A201 - 300
4X-RAY DIFFRACTION1A301 - 363
5X-RAY DIFFRACTION2B2 - 100
6X-RAY DIFFRACTION2B101 - 200
7X-RAY DIFFRACTION2B201 - 300
8X-RAY DIFFRACTION2B301 - 363
9X-RAY DIFFRACTION3C2 - 100
10X-RAY DIFFRACTION3C101 - 200
11X-RAY DIFFRACTION3C201 - 300
12X-RAY DIFFRACTION3C301 - 364
13X-RAY DIFFRACTION4D3 - 100
14X-RAY DIFFRACTION4D101 - 200
15X-RAY DIFFRACTION4D201 - 300
16X-RAY DIFFRACTION4D301 - 363

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