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- PDB-6u1j: Thermus thermophilus D-alanine-D-alanine ligase in complex with A... -

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Basic information

Entry
Database: PDB / ID: 6u1j
TitleThermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphate, D-ala-D-ala, 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 / 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 / ATP-grasp fold profile. / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / D-ALANINE / : / PHOSPHATE ION / 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. / Thompson, A.P.
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)144,73218
Polymers143,1564
Non-polymers1,57614
Water7,891438
1
A: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3669
Polymers71,5782
Non-polymers7887
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-62 kcal/mol
Surface area23030 Å2
MethodPISA
2
C: D-alanine--D-alanine ligase
D: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3669
Polymers71,5782
Non-polymers7887
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-61 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.613, 69.080, 93.792
Angle α, β, γ (deg.)71.370, 80.240, 64.320
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, 452 molecules

#2: Chemical
ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: K
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
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: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→45.23 Å / Num. obs: 63620 / % possible obs: 98.1 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.038 / Rrim(I) all: 0.075 / Net I/σ(I): 10.7 / Num. measured all: 246629 / Scaling rejects: 4
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
2.2-2.253.90.5951743644340.7820.3470.6891.697.4
10.08-45.233.40.01822096410.9990.0110.02233.995.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.48 Å44.41 Å
Translation5.48 Å44.41 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→34.847 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 3313 5.21 %
Rwork0.2189 60280 -
obs0.2211 63593 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.69 Å2 / Biso mean: 41.0861 Å2 / Biso min: 20.41 Å2
Refinement stepCycle: final / Resolution: 2.2→34.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9415 0 92 438 9945
Biso mean--38.12 40.53 -
Num. residues----1256
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2001-2.23150.31821320.2822250797
2.2315-2.26480.32921420.2751245697
2.2648-2.30020.31541420.2639255798
2.3002-2.33790.28311320.2668245998
2.3379-2.37820.29831400.2549252398
2.3782-2.42140.32851240.2568247797
2.4214-2.4680.29371400.2574253898
2.468-2.51830.28351290.2466244398
2.5183-2.57310.2991370.2487254498
2.5731-2.63290.2951620.2498247198
2.6329-2.69870.31971480.2538253698
2.6987-2.77170.30611330.2524250898
2.7717-2.85320.29941390.2435250698
2.8532-2.94520.29341510.2512252398
2.9452-3.05040.30341310.2427249198
3.0504-3.17250.22951250.2382254398
3.1725-3.31680.29081350.2348256799
3.3168-3.49150.25881370.2268251399
3.4915-3.710.26991380.2162250799
3.71-3.99610.24571650.1934250099
3.9961-4.39750.22451330.1834251798
4.3975-5.03220.16951400.1724252498
5.0322-6.33390.26531360.1958254899
6.3339-34.840.24621220.1895252298

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