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- PDB-3wo1: Crystal structure of Trp332Ala mutant YwfE, an L-amino acid ligas... -

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Basic information

Entry
Database: PDB / ID: 3wo1
TitleCrystal structure of Trp332Ala mutant YwfE, an L-amino acid ligase, with bound ADP-Mg-Ala
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, subdomain 1 / ATP-grasp fold, B domain / 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, subdomain 1 / ATP-grasp fold, B domain / 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 / ALANINE / Alanine--anticapsin ligase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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.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)52,3605
Polymers51,7951
Non-polymers5654
Water1,56787
1
A: Alanine-anticapsin ligase BacD
hetero molecules

A: Alanine-anticapsin ligase BacD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,72110
Polymers103,5912
Non-polymers1,1308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area4340 Å2
ΔGint-64 kcal/mol
Surface area36680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.129, 91.129, 258.757
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: 51795.422 Da / Num. of mol.: 1 / Fragment: UNP residues 4-468 / Mutation: W332A
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-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 16% PEG 3350, 0.3M NaCl, 0.1M HEPES-NaOH, 5% ethylene glycol, 1mM DTT, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 14, 2013 / 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: 2.3→20 Å / Num. obs: 28700 / % possible obs: 98.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 55.6
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 7.6 / Num. unique all: 1799 / % possible all: 100

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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: 2.3→19.74 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.582 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26141 1475 5.2 %RANDOM
Rwork0.22145 ---
obs0.22356 27089 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.943 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å2-2.41 Å20 Å2
2---2.41 Å20 Å2
3---7.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3623 0 35 87 3745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193732
X-RAY DIFFRACTIONr_bond_other_d0.0010.023533
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9755063
X-RAY DIFFRACTIONr_angle_other_deg0.69238175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8625465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44625.621169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30215636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3451511
X-RAY DIFFRACTIONr_chiral_restr0.080.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02796
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: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 112 -
Rwork0.282 1967 -
obs--99.52 %
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)
11.6994-0.0214-0.26511.782-0.47080.88160.1679-0.20360.10590.1433-0.2325-0.17250.0408-0.04890.06460.3303-0.09650.12050.36690.12460.14139.31495.600643.6409
22.84273.4880.73856.85710.15543.5570.2537-0.2914-0.31420.3389-0.5219-0.3941-0.0510.2320.26820.2315-0.01030.0830.33190.32650.380132.317511.82641.3464
33.11820.34870.3031.18920.11620.16120.4535-0.7658-0.09150.6017-0.3971-0.3907-0.04-0.0122-0.05640.6298-0.3551-0.0220.55290.27320.433231.749825.634650.4964
41.87091.3003-0.40981.4555-0.43060.63010.24530.04630.60420.0168-0.18740.1305-0.0583-0.0092-0.05780.24370.01130.18850.24770.20510.407815.913127.917834.0529
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 125
2X-RAY DIFFRACTION2A126 - 149
3X-RAY DIFFRACTION3A150 - 240
4X-RAY DIFFRACTION4A241 - 468

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