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- PDB-3vmm: Crystal structure of BacD, an L-amino acid dipeptide ligase from ... -

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Basic information

Entry
Database: PDB / ID: 3vmm
TitleCrystal structure of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis
ComponentsAlanine-anticapsin ligase BacD
KeywordsLIGASE / ATP-grasp domain / amino acid ligase / ATP binding
Function / homology
Function and homology information


L-alanine-L-anticapsin ligase / L-amino-acid alpha-ligase activity / antibiotic biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Aldehyde Oxidoreductase; domain 3 - #60 / ATP-grasp domain / : / Rossmann fold - #20 / Aldehyde Oxidoreductase; domain 3 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile. ...Aldehyde Oxidoreductase; domain 3 - #60 / ATP-grasp domain / : / Rossmann fold - #20 / Aldehyde Oxidoreductase; domain 3 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-P0D / Alanine--anticapsin ligase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShomura, Y. / Higuchi, Y.
CitationJournal: Protein Sci. / Year: 2012
Title: Structural and enzymatic characterization of BacD, an l-amino acid dipeptide ligase from Bacillus subtilis
Authors: Shomura, Y. / Hinokuchi, E. / Ikeda, H. / Senoo, A. / Takahashi, Y. / Saito, J. / Komori, H. / Shibata, N. / Yonetani, Y. / Higuchi, Y.
History
DepositionDec 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine-anticapsin ligase BacD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2805
Polymers52,4531
Non-polymers8274
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.787, 130.787, 147.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Alanine-anticapsin ligase BacD / Bacilysin synthetase / L-amino acid ligase


Mass: 52453.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bacD, BSU37710, ipa-83d / Production host: Escherichia coli (E. coli) / References: UniProt: P39641, EC: 6.3.2.28
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-P0D / (2S)-3-[(S)-[(1R)-1-aminoethyl](phosphonooxy)phosphoryl]-2-benzylpropanoic acid


Mass: 351.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Bis-Tris propane, 60mM sodium citrate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 29, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 26252 / Num. obs: 26252 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1277 / % possible all: 1

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.93 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 17.92 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22943 1327 5.1 %RANDOM
Rwork0.19177 ---
obs0.19375 24770 99.35 %-
all-26252 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.022 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å2-0 Å2
2--0.07 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 51 147 3873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223804
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9815166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07625.523172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77115645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6921512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212870
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3361.52354
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69423792
X-RAY DIFFRACTIONr_scbond_it1.26331450
X-RAY DIFFRACTIONr_scangle_it2.1734.51374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.502→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 77 -
Rwork0.252 1755 -
obs--97.19 %
Refinement TLS params.Method: refined / Origin x: -1.262 Å / Origin y: -46.195 Å / Origin z: -9.803 Å
111213212223313233
T0.1408 Å20.0041 Å2-0.1254 Å2-0.0546 Å2-0.0189 Å2--0.2168 Å2
L1.7772 °2-0.9044 °20.3995 °2-2.0765 °2-0.5482 °2--0.753 °2
S-0.2051 Å °-0.0723 Å °0.4367 Å °0.3005 Å °0.0358 Å °-0.5227 Å °-0.0506 Å °-0.0034 Å °0.1692 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 472
2X-RAY DIFFRACTION1A501 - 504
3X-RAY DIFFRACTION1A601 - 747

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