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- PDB-4dyj: Crystal structure of a broad specificity amino acid racemase (Bar... -

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Basic information

Entry
Database: PDB / ID: 4dyj
TitleCrystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage
Componentsbroad specificity amino acid racemase
KeywordsISOMERASE / PLP binding / Racemization
Function / homology
Function and homology information


arginine racemase activity / lysine racemase activity / amino-acid racemase / alanine racemase activity / pyridoxal phosphate binding / periplasmic space
Similarity search - Function
Racemase Bsr/Lyr / Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...Racemase Bsr/Lyr / Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Broad specificity amino-acid racemase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWang, W.C. / Wu, H.M.
CitationJournal: Plos One / Year: 2012
Title: Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants
Authors: Wu, H.M. / Kuan, Y.C. / Chu, C.H. / Hsu, W.H. / Wang, W.C.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: broad specificity amino acid racemase
B: broad specificity amino acid racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,53818
Polymers89,0092
Non-polymers1,52916
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-179 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.252, 118.740, 77.780
Angle α, β, γ (deg.)90.00, 100.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-748-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 26 - 409 / Label seq-ID: 26 - 409

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein broad specificity amino acid racemase / Bar


Mass: 44504.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: DSM84 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6LNY0*PLUS, amino-acid racemase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 3.63 Å3/Da / Density % sol: 66.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 2.0M Ammonium-Sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2011
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 57075 / Num. obs: 46692 / % possible obs: 81.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.45→2.54 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
Blu-IceControl Softwaredata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se-Met model

Resolution: 2.45→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.975 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2344 5 %RANDOM
Rwork0.15812 ---
all0.2 46445 --
obs0.1609 44101 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.413 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å20 Å2-2.78 Å2
2---3.73 Å20 Å2
3---4.82 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5870 0 82 381 6333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216036
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9638184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44423.864264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.569151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5711546
X-RAY DIFFRACTIONr_chiral_restr0.1190.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024484
X-RAY DIFFRACTIONr_mcbond_it1.74123794
X-RAY DIFFRACTIONr_mcangle_it2.91836062
X-RAY DIFFRACTIONr_scbond_it2.37622242
X-RAY DIFFRACTIONr_scangle_it3.66332122
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2935 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.220.5
medium thermal2.252
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 162 -
Rwork0.234 3164 -
obs--98.2 %

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