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- PDB-5elm: Crystal structure of L-aspartate/glutamate specific racemase in c... -

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Basic information

Entry
Database: PDB / ID: 5elm
TitleCrystal structure of L-aspartate/glutamate specific racemase in complex with L-glutamate
ComponentsAsp/Glu_racemase family protein
KeywordsISOMERASE / Asp/Glu racemase / L-form specific racemase / amino acid enantiomers
Function / homology
Function and homology information


aspartate racemase / aspartate racemase activity / amino-acid racemase / amino-acid racemase activity / glutamate racemase / glutamate racemase activity / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / : / identical protein binding
Similarity search - Function
Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold ...Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / NITRATE ION / L-aspartate/glutamate-specific racemase / Amino acid racemase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAhn, J.W. / Chang, J.H. / Kim, K.J.
CitationJournal: Febs Lett. / Year: 2015
Title: Structural basis for an atypical active site of an l-aspartate/glutamate-specific racemase from Escherichia coli
Authors: Ahn, J.W. / Chang, J.H. / Kim, K.J.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Asp/Glu_racemase family protein
B: Asp/Glu_racemase family protein
C: Asp/Glu_racemase family protein
D: Asp/Glu_racemase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,24410
Polymers105,5564
Non-polymers6886
Water10,611589
1
A: Asp/Glu_racemase family protein
B: Asp/Glu_racemase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0174
Polymers52,7782
Non-polymers2392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-14 kcal/mol
Surface area18570 Å2
MethodPISA
2
C: Asp/Glu_racemase family protein
D: Asp/Glu_racemase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2266
Polymers52,7782
Non-polymers4484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-10 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.530, 81.250, 83.960
Angle α, β, γ (deg.)90.00, 111.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Asp/Glu_racemase family protein / Aspartate racemase / Putative racemase / Putative resistance proteins / Racemase / Strain O157 ...Aspartate racemase / Putative racemase / Putative resistance proteins / Racemase / Strain O157 SvETEC scaffold16.1 / whole genome shotgun sequence


Mass: 26389.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: C3SWD2, UniProt: A0A140N890*PLUS, aspartate racemase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.03 Å3/Da / Density % sol: 39.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.3 M ammonium nitrate, 14~16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 56118 / % possible obs: 98.3 % / Redundancy: 3.3 % / Net I/σ(I): 6
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.9 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ELL

5ell


Resolution: 2→29.32 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.885 / SU B: 4.228 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 2833 5.1 %RANDOM
Rwork0.17328 ---
obs0.17644 53262 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.241 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7274 0 46 589 7909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197531
X-RAY DIFFRACTIONr_bond_other_d0.0010.027236
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.95410181
X-RAY DIFFRACTIONr_angle_other_deg0.903316571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8775952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45823.408355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.286151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2341565
X-RAY DIFFRACTIONr_chiral_restr0.1050.21149
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021780
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_it1.8041.9233805
X-RAY DIFFRACTIONr_mcbond_other1.7981.9233804
X-RAY DIFFRACTIONr_mcangle_it2.7532.874758
X-RAY DIFFRACTIONr_mcangle_other2.7542.874759
X-RAY DIFFRACTIONr_scbond_it2.3262.2533726
X-RAY DIFFRACTIONr_scbond_other2.3262.2533726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7093.2745424
X-RAY DIFFRACTIONr_long_range_B_refined6.64616.6739139
X-RAY DIFFRACTIONr_long_range_B_other6.64616.6739139
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 185 -
Rwork0.175 3780 -
obs--94.18 %

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