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- PDB-6dgi: The crystal structure of D-alanyl-alanine synthetase A from Vibri... -

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Basic information

Entry
Database: PDB / ID: 6dgi
TitleThe crystal structure of D-alanyl-alanine synthetase A from Vibrio cholerae O1 biovar eltor str. N16961
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
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. / ATP-grasp fold, A domain / ATP-grasp fold, B 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. / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsTan, K. / Zhou, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: The crystal structure of D-alanyl-alanine synthetase A from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Tan, K. / Zhou, M. / Joachimiak, A.
History
DepositionMay 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,2977
Polymers76,0052
Non-polymers2925
Water1,982110
1
B: D-alanine--D-alanine ligase
hetero molecules

A: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2977
Polymers76,0052
Non-polymers2925
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4210 Å2
ΔGint-38 kcal/mol
Surface area28900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.588, 64.875, 165.160
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 / D-Ala-D-Ala ligase / D-alanylalanine synthetase


Mass: 38002.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: ddl, VC_A0572 / Plasmid: pMCSG19C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: Q9KM17, D-alanine-D-alanine ligase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 0.2M magnesium format, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2014
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.3→44 Å / Num. obs: 30876 / % possible obs: 96.9 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 25.35 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.035 / Rrim(I) all: 0.079 / Χ2: 0.698 / Net I/σ(I): 22.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 5.51 / Num. unique obs: 1533 / CC1/2: 0.782 / Rpim(I) all: 0.357 / Rrim(I) all: 0.788 / Χ2: 0.782 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementResolution: 2.3→43.787 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 1429 4.75 %random
Rwork0.1772 ---
obs0.1792 30054 96.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→43.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5171 0 18 110 5299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045324
X-RAY DIFFRACTIONf_angle_d0.6327221
X-RAY DIFFRACTIONf_dihedral_angle_d6.7174376
X-RAY DIFFRACTIONf_chiral_restr0.044803
X-RAY DIFFRACTIONf_plane_restr0.004929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.26981260.20372735X-RAY DIFFRACTION93
2.3822-2.47760.28331400.20922782X-RAY DIFFRACTION95
2.4776-2.59040.27321500.21012822X-RAY DIFFRACTION97
2.5904-2.72690.25511530.20752843X-RAY DIFFRACTION98
2.7269-2.89770.24871360.21122890X-RAY DIFFRACTION98
2.8977-3.12140.23421400.20272875X-RAY DIFFRACTION98
3.1214-3.43540.20091510.19042874X-RAY DIFFRACTION97
3.4354-3.93230.19341350.16242923X-RAY DIFFRACTION97
3.9323-4.95310.18011290.1382939X-RAY DIFFRACTION97
4.9531-43.79460.20821690.15822942X-RAY DIFFRACTION94
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)
11.4001-0.537-0.35890.58030.51211.9540.06010.2581-0.0384-0.44940.03710.20820.1216-0.2973-0.06280.4471-0.1014-0.12010.33480.06390.211745.86142.32544.3186
21.8961-0.0899-0.27651.1326-0.20991.0045-0.0819-0.08760.06380.05110.07990.19660.0393-0.10770.01560.1378-0.0255-0.01660.16750.01080.312739.238210.474831.7834
32.05742.5383-0.66477.0615-0.02020.4597-0.04890.37280.5195-0.16860.14610.54570.2362-0.23970.04580.34580.06110.05330.50790.16280.633323.229614.406420.029
42.2759-0.1951-0.4772.19910.75462.51980.14230.28020.5342-0.5980.15050.4055-0.3381-0.245-0.18650.3141-0.0099-0.09440.22970.14890.373141.380520.640415.8255
51.22250.22140.2041.22210.34541.9808-0.0360.2697-0.0239-0.31670.0233-0.02550.22120.0386-0.01040.2127-0.00330.00520.19050.01980.136464.6911-2.003618.3063
60.9089-0.1464-0.22690.1401-0.24270.6783-0.00810.02370.1351-0.0117-0.0622-0.2301-0.06340.22280.07190.1859-0.0363-0.03580.2370.02890.278576.33049.153429.7644
71.8845-0.16220.89633.7741.7093.2579-0.020.0231-0.00110.00920.0052-0.09020.22380.05480.01160.1373-0.00360.0350.11560.04340.139368.6727-4.081634.6198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 116 )
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 233 )
3X-RAY DIFFRACTION3chain 'A' and (resid 234 through 254 )
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 332 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 155 )
6X-RAY DIFFRACTION6chain 'B' and (resid 156 through 254 )
7X-RAY DIFFRACTION7chain 'B' and (resid 255 through 333 )

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