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- PDB-3dxw: The crystal structure of alpha-amino-epsilon-caprolactam racemase... -

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Basic information

Entry
Database: PDB / ID: 3dxw
TitleThe crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam
ComponentsAlpha-amino-epsilon-caprolactam racemase
KeywordsISOMERASE / fold-type1 / pyridoxal-5'-phosphate dependent racemase / Pyridoxal phosphate
Function / homology
Function and homology information


2-aminohexano-6-lactam racemase / 2-aminohexano-6-lactam racemase activity / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
azepan-2-one / PYRIDOXAL-5'-PHOSPHATE / 2-aminohexano-6-lactam racemase
Similarity search - Component
Biological speciesAchromobacter obae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsOkazaki, S. / Suzuki, A. / Komeda, H. / Asano, Y. / Yamane, T.
CitationJournal: Biochemistry / Year: 2009
Title: The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae
Authors: Okazaki, S. / Suzuki, A. / Mizushima, T. / Kawano, T. / Komeda, H. / Asano, Y. / Yamane, T.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Alpha-amino-epsilon-caprolactam racemase
B: Alpha-amino-epsilon-caprolactam racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8376
Polymers95,1162
Non-polymers7214
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-58.2 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.581, 60.653, 105.315
Angle α, β, γ (deg.)90.00, 103.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-amino-epsilon-caprolactam racemase


Mass: 47558.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter obae (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7M181, Isomerases; Racemases and epimerases
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-ICC / azepan-2-one


Mass: 113.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.85 Å3/Da / Density % sol: 33.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 30% PEG4000, 0.2M magnesium chloride, 0.1M Tris/HCl(pH8.7), 2.9% Sucrose, 42microM PLP, 20mM epsilon-caprolactam, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: May 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 26897 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.088 / Rsym value: 0.073
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5 % / Rmerge(I) obs: 0.359 / Rsym value: 0.32 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFT

1sft


Resolution: 2.41→40.29 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.476 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 6.638 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25232 1348 5 %RANDOM
Rwork0.19126 ---
obs0.19434 25532 98.6 %-
all-26897 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.41→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 46 56 6374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9868756
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7035844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37922.795254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.24115988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8631552
X-RAY DIFFRACTIONr_chiral_restr0.0840.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024922
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.23072
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24380
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6091.54294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0926637
X-RAY DIFFRACTIONr_scbond_it1.56932403
X-RAY DIFFRACTIONr_scangle_it2.6374.52119
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.406→2.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 100 -
Rwork0.27 1830 -
obs--96.07 %

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