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- PDB-1xpy: Structural Basis for Catalytic Racemization and Substrate Specifi... -

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Basic information

Entry
Database: PDB / ID: 1xpy
TitleStructural Basis for Catalytic Racemization and Substrate Specificity of an N-Acylamino Acid Racemase Homologue from Deinococcus radiodurans
ComponentsN-acylamino acid racemase
KeywordsISOMERASE / RACEMASE
Function / homology
Function and homology information


O-succinylbenzoate synthase activity / o-succinylbenzoate synthase / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / menaquinone biosynthetic process / isomerase activity / metal ion binding
Similarity search - Function
o-Succinylbenzoate synthase, MenC type 2 / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal ...o-Succinylbenzoate synthase, MenC type 2 / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N~2~-ACETYL-L-GLUTAMINE / N-succinylamino acid racemase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, W.-C. / Chiu, W.-C. / Hsu, S.-K. / Wu, C.-L. / Chen, C.-Y. / Liu, J.-S. / Hsu, W.-H.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans
Authors: Wang, W.-C. / Chiu, W.-C. / Hsu, S.-K. / Wu, C.-L. / Chen, C.-Y. / Liu, J.-S. / Hsu, W.-H.
History
DepositionOct 10, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: N-acylamino acid racemase
B: N-acylamino acid racemase
C: N-acylamino acid racemase
D: N-acylamino acid racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,71610
Polymers164,2434
Non-polymers4746
Water15,169842
1
A: N-acylamino acid racemase
C: N-acylamino acid racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3585
Polymers82,1212
Non-polymers2373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acylamino acid racemase
D: N-acylamino acid racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3585
Polymers82,1212
Non-polymers2373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.159, 116.159, 120.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
N-acylamino acid racemase


Mass: 41060.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Plasmid: NAAAR-PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9RYA6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NLQ / N~2~-ACETYL-L-GLUTAMINE / N-ACETYL-L-GLUTAMINE


Type: L-peptide linking / Mass: 188.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 842 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: lithium sulfate, PEG 4000, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 1416552 / Num. obs: 66037 / % possible obs: 98.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.38 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R0M

1r0m


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.712 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22742 3511 5 %RANDOM
Rwork0.17121 ---
obs0.17399 66037 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.881 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11236 0 30 842 12108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02111472
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210776
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.95915562
X-RAY DIFFRACTIONr_angle_other_deg0.745324840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44951454
X-RAY DIFFRACTIONr_chiral_restr0.0760.21756
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212920
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022374
X-RAY DIFFRACTIONr_nbd_refined0.2280.32556
X-RAY DIFFRACTIONr_nbd_other0.2620.313167
X-RAY DIFFRACTIONr_nbtor_other0.0890.57131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.51193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0820.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.3101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.546
X-RAY DIFFRACTIONr_mcbond_it0.99527232
X-RAY DIFFRACTIONr_mcangle_it1.692311558
X-RAY DIFFRACTIONr_scbond_it0.99124240
X-RAY DIFFRACTIONr_scangle_it1.69434004
LS refinement shellResolution: 2.302→2.362 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 -
Rwork0.18 4899

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