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- PDB-3r5x: Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus an... -

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Basic information

Entry
Database: PDB / ID: 3r5x
TitleCrystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / alpha-beta structure / cytosol / Structural Genomics / 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 / cytoplasm
Similarity search - Function
Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / Rossmann fold - #20 ...Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / 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
ACETIC ACID / ADENOSINE-5'-TRIPHOSPHATE / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKim, Y. / Mulligan, R. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP
Authors: Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 1, 2014Group: Database references / Structure summary
Revision 1.3Jun 24, 2015Group: Other
Revision 1.4Jul 1, 2015Group: Derived calculations

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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
B: D-alanine--D-alanine ligase
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,72718
Polymers139,2714
Non-polymers2,45614
Water13,511750
1
A: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7707
Polymers69,6362
Non-polymers1,1355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-19 kcal/mol
Surface area27270 Å2
MethodPISA
2
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,95711
Polymers69,6362
Non-polymers1,3219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-18 kcal/mol
Surface area26510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.336, 68.992, 92.387
Angle α, β, γ (deg.)73.36, 84.96, 75.46
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 34817.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS2435, BA_2610, ddl, ddlB, GBAA_2610 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81Q29, D-alanine-D-alanine ligase

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Non-polymers , 6 types, 764 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS pH 6.5, 20 % w/v Polyethylene glycol monomethyl ether 5000, 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: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 84177 / Num. obs: 84177 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 37.17 Å2 / Rsym value: 0.087 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.84 / Num. unique all: 4022 / Rsym value: 0.408 / % possible all: 93.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→32.775 Å / SU ML: 0.28 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4235 5.04 %random
Rwork0.177 ---
all0.18 84091 --
obs0.18 84091 96.85 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.251 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.0283 Å2-2.2671 Å25.5796 Å2
2---2.2184 Å2-16.28 Å2
3---3.2467 Å2
Refinement stepCycle: LAST / Resolution: 2→32.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9215 0 140 750 10105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019789
X-RAY DIFFRACTIONf_angle_d1.28413253
X-RAY DIFFRACTIONf_dihedral_angle_d16.8673781
X-RAY DIFFRACTIONf_chiral_restr0.0851511
X-RAY DIFFRACTIONf_plane_restr0.0071677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2-2.02540.35991240.31772369249386
2.0254-2.04920.34231450.3062558270394
2.0492-2.07420.3151430.28762639278295
2.0742-2.10040.29911380.27092663280196
2.1004-2.12810.32321360.26682626276297
2.1281-2.15720.30491460.2522739288597
2.1572-2.1880.29771480.23882586273497
2.188-2.22070.26031480.23332682283097
2.2207-2.25540.33371420.23792690283297
2.2554-2.29230.27831530.21982635278897
2.2923-2.33180.25441450.2072684282998
2.3318-2.37420.26511470.1962690283797
2.3742-2.41990.28161410.22672281398
2.4199-2.46930.25891130.20592720283398
2.4693-2.52290.29671280.20762686281498
2.5229-2.58160.26861210.19082721284298
2.5816-2.64610.24711600.19462702286298
2.6461-2.71760.28231240.18782663278798
2.7176-2.79760.23071390.18282731287098
2.7976-2.88780.23341500.17822663281398
2.8878-2.9910.25491270.18252752287998
2.991-3.11060.24531590.19162684284398
3.1106-3.25210.2361480.180126792858282798
3.2521-3.42340.19931410.1782701284298
3.4234-3.63760.20591560.1672702285898
3.6376-3.9180.18331660.15432654282098
3.918-4.31150.15821500.13482754290499
4.3115-4.93360.17671370.12522694283199
4.9336-6.20890.18761530.15712705285899
6.2089-32.77960.19051070.16872412251987
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)
10.87-0.3988-0.47490.96110.97260.895-0.0092-0.0262-0.18380.1956-0.020.11420.10360.01330.03290.3555-0.00670.01930.25630.0240.283685.577174.3076-4.7055
21.0150.0778-0.30541.24121.28940.91140.165-0.20850.15910.26890.02130.0727-0.14010.2373-0.04150.4671-0.06160.050.3404-0.02760.236486.665596.973315.8858
30.95250.2950.16110.96930.93062.0302-0.07730.2627-0.1927-0.07920.158-0.23330.1446-0.048-0.03820.2909-0.03940.03640.2646-0.03370.295746.047846.388943.2259
40.55740.41790.11941.46510.75531.37310.03390.06950.23550.05910.1062-0.23090.06280.0211-0.02290.11480.0428-0.04080.2415-0.05860.379657.322371.658855.5291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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