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- PDB-5m4d: Alpha-amino epsilon-caprolactam racemase K241A mutant in complex ... -

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Basic information

Entry
Database: PDB / ID: 5m4d
TitleAlpha-amino epsilon-caprolactam racemase K241A mutant in complex with D-ACL (external aldimine)
ComponentsAminotransferase class-III
KeywordsISOMERASE / PLP / racemase
Function / homology
Function and homology information


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
Chem-7F7 / Aminotransferase class-III
Similarity search - Component
Biological speciesRhizobium freirei PRF 81 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsFrese, A. / Sutton, P.W. / Turkenburg, J.P. / Grogan, G.
CitationJournal: Acs Catalysis / Year: 2017
Title: Snapshots of the Catalytic Cycle of the Industrial Enzyme alpha-Amino-epsilon-Caprolactam Racemase (ACLR) Observed Using X-ray Crystallography
Authors: Frese, A. / Sutton, P.W. / Turkenburg, J.P. / Grogan, G.
History
DepositionOct 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase class-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4666
Polymers45,8601
Non-polymers6065
Water1,856103
1
A: Aminotransferase class-III
hetero molecules

A: Aminotransferase class-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,93112
Polymers91,7202
Non-polymers1,21110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8980 Å2
ΔGint-38 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.100, 77.490, 58.520
Angle α, β, γ (deg.)90.00, 113.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-637-

HOH

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Components

#1: Protein Aminotransferase class-III


Mass: 45860.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium freirei PRF 81 (bacteria) / Gene: RHSP_08934 / Plasmid: pET-YSBLIC-3C / Production host: Escherichia coli (E. coli) / References: UniProt: N6UXY4
#2: Chemical ChemComp-7F7 / [6-methyl-5-oxidanyl-4-[(~{E})-[(3~{R})-2-oxidanylideneazepan-3-yl]iminomethyl]pyridin-3-yl]methyl dihydrogen phosphate


Mass: 357.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N3O6P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M MgCl2, 25 % PEG 3350, 0.1 mM HEPES (pH 7.0).

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.86→55.27 Å / Num. obs: 29415 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 1.3
Reflection shellResolution: 1.86→1.91 Å / Rmerge(I) obs: 0.88 / Num. unique all: 2171

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZUK

2zuk


Resolution: 1.93→55.27 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.368 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25066 1281 4.9 %RANDOM
Rwork0.19325 ---
obs0.19597 25058 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0.21 Å2
2---1.5 Å2-0 Å2
3---1.19 Å2
Refinement stepCycle: 1 / Resolution: 1.93→55.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 44 103 3348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193315
X-RAY DIFFRACTIONr_bond_other_d0.0030.023187
X-RAY DIFFRACTIONr_angle_refined_deg2.0141.984501
X-RAY DIFFRACTIONr_angle_other_deg1.1573.0017305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98523.047128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14215490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4111525
X-RAY DIFFRACTIONr_chiral_restr0.1270.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213827
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02734
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_it0.9241.3491765
X-RAY DIFFRACTIONr_mcbond_other0.9241.3491764
X-RAY DIFFRACTIONr_mcangle_it1.3912.0192205
X-RAY DIFFRACTIONr_mcangle_other1.3912.0192206
X-RAY DIFFRACTIONr_scbond_it1.3731.5261550
X-RAY DIFFRACTIONr_scbond_other1.3731.5261550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0762.2162296
X-RAY DIFFRACTIONr_long_range_B_refined3.30611.1933793
X-RAY DIFFRACTIONr_long_range_B_other3.30611.1963794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 115 -
Rwork0.255 1825 -
obs--99.54 %

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