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- PDB-5bpf: Crystal structure of ADP complexed D-alanine-D-alanine ligase(DDL... -

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Basic information

Entry
Database: PDB / ID: 5bpf
TitleCrystal structure of ADP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis
ComponentsD-alanine-D-alanine ligase
KeywordsLIGASE / D-alanine-D-alanine ligase (DDL) / drug target / bacterial cell wall synthesis / Yersinia pestis
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
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsTran, H.T. / Kang, L.W. / Hong, M.K.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
Authors: Tran, H.T. / Hong, M.K. / Ngo, H.P. / Huynh, K.H. / Ahn, Y.J. / Wang, Z. / Kang, L.W.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

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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)134,81221
Polymers132,7194
Non-polymers2,09317
Water7,386410
1
A: D-alanine-D-alanine ligase
B: D-alanine-D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,15810
Polymers66,3602
Non-polymers7988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-50 kcal/mol
Surface area25940 Å2
MethodPISA
2
C: D-alanine-D-alanine ligase
D: D-alanine-D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,65411
Polymers66,3602
Non-polymers1,2959
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-63 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.872, 106.475, 211.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 33179.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ddl, ddlB, YPO0557, y3624, YP_3627 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8ZIE7, D-alanine-D-alanine ligase

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Non-polymers , 5 types, 427 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.67 Å3/Da / Density % sol: 53.87 % / Description: orthorhombic shaped crystal
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M sodium acetate, 0.1 M Bis-Tris pH 7.0, 29% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2013
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 64040 / % possible obs: 99.9 % / Redundancy: 7.21 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 33.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQI

4zqi


Resolution: 2.28→37.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.147 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25288 3336 5.1 %RANDOM
Rwork0.18555 ---
obs0.18895 62408 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.005 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.28→37.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9086 0 132 410 9628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0199412
X-RAY DIFFRACTIONr_bond_other_d0.0020.029022
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.99712737
X-RAY DIFFRACTIONr_angle_other_deg0.843320802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25551184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96225.026378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.333151572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0681536
X-RAY DIFFRACTIONr_chiral_restr0.10.21461
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021981
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.953.4174773
X-RAY DIFFRACTIONr_mcbond_other2.9453.4164770
X-RAY DIFFRACTIONr_mcangle_it4.4555.0965942
X-RAY DIFFRACTIONr_mcangle_other4.4555.0965943
X-RAY DIFFRACTIONr_scbond_it3.8264.0084639
X-RAY DIFFRACTIONr_scbond_other3.8244.0084639
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9875.8196796
X-RAY DIFFRACTIONr_long_range_B_refined7.93728.01410717
X-RAY DIFFRACTIONr_long_range_B_other7.93728.01510717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 241 -
Rwork0.209 4565 -
obs--100 %

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