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- PDB-3wnz: Crystal structure of Bacillus subtilis YwfE, an L-amino acid liga... -

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Basic information

Entry
Database: PDB / ID: 3wnz
TitleCrystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Pi
ComponentsAlanine-anticapsin ligase BacD
KeywordsLIGASE / ATP-grasp Fold / 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. / D-amino Acid Aminotransferase; Chain A, domain 1 ...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 / PHOSPHATE ION / Alanine--anticapsin ligase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsTsuda, T. / Kojima, S.
CitationJournal: Biochemistry / Year: 2014
Title: Single Mutation Alters the Substrate Specificity of l-Amino Acid Ligase
Authors: Tsuda, T. / Asami, M. / Koguchi, Y. / Kojima, S.
History
DepositionDec 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2014Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Alanine-anticapsin ligase BacD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4815
Polymers51,9111
Non-polymers5714
Water7,134396
1
A: Alanine-anticapsin ligase BacD
hetero molecules

A: Alanine-anticapsin ligase BacD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,96310
Polymers103,8212
Non-polymers1,1428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area4650 Å2
ΔGint-89 kcal/mol
Surface area35750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.581, 90.581, 252.654
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: 51910.555 Da / Num. of mol.: 1 / Fragment: UNP residues 4-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ywfe / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress RIL (DE3) / References: UniProt: P39641, EC: 6.3.2.28
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG 3350, 0.3M NaCl, 0.1M HEPES-NaOH, 5% ethylene glycol, 1mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2012 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 43922 / % possible obs: 88.9 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 53.5
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 9.9 / Num. unique all: 3319 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
CRANKphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→17.42 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.238 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24301 2232 5.1 %RANDOM
Rwork0.19658 ---
obs0.19899 41606 88.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.552 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å2-1.24 Å20 Å2
2---1.24 Å20 Å2
3---4.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 34 396 4056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193736
X-RAY DIFFRACTIONr_bond_other_d0.0010.023527
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9745071
X-RAY DIFFRACTIONr_angle_other_deg0.70438161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4775464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49625.588170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92315636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8651511
X-RAY DIFFRACTIONr_chiral_restr0.090.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02801
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 181 -
Rwork0.247 3213 -
obs--96.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.63720.3277-0.00021.5495-0.26720.73610.1971-0.09820.1460.2258-0.15220.08140.0669-0.0418-0.0450.2322-0.02430.16450.1930.10980.21059.98164.560142.9114
23.07262.25210.11465.79281.03792.40450.2647-0.1272-0.02420.3504-0.5497-0.5376-0.00890.25410.2850.1736-0.02340.04820.190.22970.312932.667111.228240.8886
30.6995-0.6964-0.05331.5355-0.29220.73620.0035-0.12840.28230.5192-0.0565-0.1919-0.2190.06510.05290.3538-0.1020.07990.23140.11050.353531.927924.548349.9612
41.74941.4666-0.16511.9199-0.32990.21650.28270.00330.60710.2032-0.19720.3587-0.01870.008-0.08550.1880.02260.21010.15340.15070.422916.605426.7633.5079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 125
2X-RAY DIFFRACTION2A126 - 149
3X-RAY DIFFRACTION3A150 - 240
4X-RAY DIFFRACTION4A241 - 468

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