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- PDB-6u1k: Thermus thermophilus D-alanine-D-alanine ligase in complex with A... -

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Basic information

Entry
Database: PDB / ID: 6u1k
TitleThermus thermophilus D-alanine-D-alanine ligase in complex with ADP, carbonate, D-alanine-D-alanine, Mg2+ and K+
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 / cytoplasm
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, subdomain 1 / Pre-ATP-grasp domain superfamily ...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, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CARBONATE ION / D-ALANINE / : / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.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
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)146,16832
Polymers143,1564
Non-polymers3,01228
Water14,484804
1
A: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,08416
Polymers71,5782
Non-polymers1,50614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-80 kcal/mol
Surface area22290 Å2
MethodPISA
2
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,08416
Polymers71,5782
Non-polymers1,50614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-80 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.909, 68.174, 90.641
Angle α, β, γ (deg.)70.790, 79.220, 66.210
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: 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

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Non-polymers , 6 types, 832 molecules

#2: Chemical
ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#5: 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
#6: Chemical
ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.55 %
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: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.67→48.15 Å / Num. obs: 127289 / % possible obs: 96.8 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.074 / Rrim(I) all: 0.139 / Net I/σ(I): 6.2 / Num. measured all: 430702 / Scaling rejects: 3
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
1.67-1.73.11.4961908961680.3021.0111.8110.895
9.15-48.153.60.04927547700.9950.030.05721.296.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.63 Å48.15 Å
Translation3.63 Å48.15 Å

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZDH

2zdh


Resolution: 1.67→43.575 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2536 6306 4.96 %
Rwork0.2181 120919 -
obs0.2199 127225 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.64 Å2 / Biso mean: 23.9075 Å2 / Biso min: 7.97 Å2
Refinement stepCycle: final / Resolution: 1.67→43.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9726 0 180 804 10710
Biso mean--18.01 29.4 -
Num. residues----1289
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.67-1.6890.40732040.3474386995
1.689-1.70890.37052200.3345401095
1.7089-1.72970.36981990.3276395695
1.7297-1.75160.33072400.3043399795
1.7516-1.77460.30532010.2993390695
1.7746-1.79890.35622180.2843398296
1.7989-1.82470.32451940.2943398196
1.8247-1.85190.33882400.2851400897
1.8519-1.88080.36231900.2937402996
1.8808-1.91170.30412310.276403296
1.9117-1.94460.30442110.2634404796
1.9446-1.980.32822060.25400597
1.98-2.01810.2692150.2319400397
2.0181-2.05930.25862130.2155406797
2.0593-2.1040.23511960.2117406697
2.104-2.1530.29461860.2135407197
2.153-2.20680.27562180.224401897
2.2068-2.26650.27172020.2131405397
2.2665-2.33320.26582380.2112401797
2.3332-2.40850.27342130.219409097
2.4085-2.49450.26272080.2112405497
2.4945-2.59440.25352040.2178406898
2.5944-2.71250.2492010.2175412098
2.7125-2.85550.25442100.2123405598
2.8555-3.03430.27021890.2284410298
3.0343-3.26850.24942130.208405498
3.2685-3.59730.22742250.1995405197
3.5973-4.11750.19892040.1796404797
4.1175-5.18630.18171960.1713410598
5.1863-43.5750.19982210.1931405698

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