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- PDB-2efx: The crystal structure of D-amino acid amidase from Ochrobactrum a... -

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Basic information

Entry
Database: PDB / ID: 2efx
TitleThe crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine amide
ComponentsD-amino acid amidase
KeywordsHYDROLASE / penicillin recognizing proteins / D-stereospecific amidase / L-phenylalanine amide
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHENYLALANINE AMIDE / D-Amino acid amidase
Similarity search - Component
Biological speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOkazaki, S. / Suzuki, A. / Mizushima, T. / Komeda, H. / Asano, Y. / Yamane, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of D-amino-acid amidase complexed with L-phenylalanine and with L-phenylalanine amide: insight into the D-stereospecificity of D-amino-acid amidase from Ochrobactrum anthropi SV3.
Authors: Okazaki, S. / Suzuki, A. / Mizushima, T. / Komeda, H. / Asano, Y. / Yamane, T.
History
DepositionFeb 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: D-amino acid amidase
B: D-amino acid amidase
C: D-amino acid amidase
D: D-amino acid amidase
E: D-amino acid amidase
F: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,77034
Polymers240,7636
Non-polymers4,00628
Water21,4021188
1
A: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8416
Polymers40,1271
Non-polymers7145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8416
Polymers40,1271
Non-polymers7145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8416
Polymers40,1271
Non-polymers7145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8416
Polymers40,1271
Non-polymers7145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7035
Polymers40,1271
Non-polymers5764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: D-amino acid amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7035
Polymers40,1271
Non-polymers5764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.711, 123.396, 115.477
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
D-amino acid amidase / DAA


Mass: 40127.191 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: SV3 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9LCC8
#2: Chemical...
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Ba
#3: Chemical
ChemComp-NFA / PHENYLALANINE AMIDE


Type: L-peptide linking / Mass: 164.204 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H12N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1188 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.04 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 103243 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.06
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.265 / Rsym value: 0.243 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUM 315data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DAA native structure (2DRW)

2drw


Resolution: 2.2→19.82 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.555 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25613 5162 5 %RANDOM
Rwork0.18689 ---
obs0.19035 97895 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.168 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16144 0 94 1188 17426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02116612
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.95222481
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5952054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47723.968761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.943152705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.711599
X-RAY DIFFRACTIONr_chiral_restr0.0940.22393
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.28350
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.211106
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.21317
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3740.226
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5921.510308
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.093216501
X-RAY DIFFRACTIONr_scbond_it1.6836400
X-RAY DIFFRACTIONr_scangle_it2.6154.55980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 336 -
Rwork0.217 5990 -
obs--82.6 %

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