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- PDB-6u1c: Apo form of Thermus thermophilus D-alanine-D-alanine ligase -

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Basic information

Entry
Database: PDB / ID: 6u1c
TitleApo form of Thermus thermophilus D-alanine-D-alanine ligase
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / ATP-grasp domain / ATP binding / metal binding
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, 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 ...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, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / 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
D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPederick, J.L. / Bruning, J.B.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations.
Authors: Pederick, J.L. / Thompson, A.P. / Bell, S.G. / Bruning, J.B.
History
DepositionAug 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)143,1564
Polymers143,1564
Non-polymers00
Water2,954164
1
A: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)71,5782
Polymers71,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-26 kcal/mol
Surface area22790 Å2
MethodPISA
2
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase


Theoretical massNumber of molelcules
Total (without water)71,5782
Polymers71,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-25 kcal/mol
Surface area22570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.866, 68.688, 91.789
Angle α, β, γ (deg.)68.310, 79.710, 65.990
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35788.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: ddl, TTHA1587 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SHZ3, D-alanine-D-alanine ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 15-18% PEG 3350, 100 mM Bis-Tris pH 6.8, 100 mM magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→43.14 Å / Num. obs: 57551 / % possible obs: 97.9 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.049 / Rrim(I) all: 0.097 / Net I/σ(I): 7.9 / Num. measured all: 223342 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.263.90.7821754144800.7170.4570.9061.497.5
9.59-43.143.70.02825076780.9990.0170.03328.496.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.36 Å42.62 Å
Translation5.36 Å42.62 Å

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZDH

2zdh


Resolution: 2.2→33.253 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 32.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 2982 5.18 %
Rwork0.238 54534 -
obs0.2395 57516 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.3 Å2 / Biso mean: 46.6263 Å2 / Biso min: 22.25 Å2
Refinement stepCycle: final / Resolution: 2.2→33.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8903 0 0 164 9067
Biso mean---43.68 -
Num. residues----1213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.23610.36331690.347260397
2.2361-2.27460.36131530.3519251397
2.2746-2.3160.35451530.3324259097
2.316-2.36050.36361340.316260997
2.3605-2.40870.32511140.3046258998
2.4087-2.4610.35181340.2982261297
2.461-2.51830.35631330.2934261598
2.5183-2.58120.35281160.2929260398
2.5812-2.6510.29481390.2869260398
2.651-2.72890.31071510.286258698
2.7289-2.8170.30241410.2704258298
2.817-2.91760.30331250.2728264998
2.9176-3.03430.29321390.2884255098
3.0343-3.17230.30331400.2692266098
3.1723-3.33940.2811530.2478255298
3.3394-3.54850.23731340.241262698
3.5485-3.82210.26931530.2146260798
3.8221-4.2060.21491550.1886257498
4.206-4.81310.21160.1812261898
4.8131-6.0580.23741470.1988262599
6.058-33.250.2181830.1962256898

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