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- PDB-5fjo: N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: G291D-... -

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Basic information

Entry
Database: PDB / ID: 5fjo
TitleN-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: G291D- F323Y mutant in complex with N-acetyl naphthylalanine
ComponentsN-succinylamino acid racemase
KeywordsLYASE / RACEMASE / ACYL AMINO ACID / ISOMERASE / AMYCOLATOPSIS
Function / homology
Function and homology information


o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / 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-acetyl naphthylalanine / N-succinylamino acid racemase
Similarity search - Component
Biological speciesAmycolatopsis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsSanchez-Carron, G. / Campopiano, D. / Grogan, G.
CitationJournal: To be Published
Title: Structure of N-Acylamino Acid Racemase Mutants in Complex with Substrates
Authors: Sanchez-Carron, G. / Campopiano, D. / Grogan, G.
History
DepositionOct 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _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-succinylamino acid racemase
B: N-succinylamino acid racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6086
Polymers79,0452
Non-polymers5634
Water15,799877
1
A: N-succinylamino acid racemase
B: N-succinylamino acid racemase
hetero molecules

A: N-succinylamino acid racemase
B: N-succinylamino acid racemase
hetero molecules

A: N-succinylamino acid racemase
B: N-succinylamino acid racemase
hetero molecules

A: N-succinylamino acid racemase
B: N-succinylamino acid racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,43124
Polymers316,1788
Non-polymers2,25316
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area20370 Å2
ΔGint-125.7 kcal/mol
Surface area93220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.710, 164.710, 169.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-2082-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8742, -0.4856, 0.005101), (-0.4856, -0.8741, 0.00839), (0.000385, -0.009811, -1)
Vector: -0.1721, -0.2264, 83.07)

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Components

#1: Protein N-succinylamino acid racemase / NSAR / N-acylamino acid racemase / AAR / NAAAR / o-succinylbenzoate synthase / OSB synthase / OSBS


Mass: 39522.305 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis sp. (bacteria) / Strain: TS-1-60 / Gene: Aaar / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q44244, Isomerases; Racemases and epimerases; Acting on amino acids and derivatives, o-succinylbenzoate synthase
#2: Chemical ChemComp-NPQ / N-acetyl naphthylalanine


Mass: 257.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15NO3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / 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: 3.69 Å3/Da / Density % sol: 66.7 % / Description: NONE
Crystal growpH: 8
Details: 100 MM TRIS HCL PH 8.0, 15% PEG 4K, 800 MM SODIUM FORMATE, PROTEIN AT 8 MG PER ML

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorDate: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.08→68.55 Å / Num. obs: 69708 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 15.5
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A6G

4a6g


Resolution: 2.08→68.55 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.8 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17465 3520 5 %RANDOM
Rwork0.14456 ---
obs0.14606 66185 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.579 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.08→68.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5546 0 40 877 6463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195704
X-RAY DIFFRACTIONr_bond_other_d0.0060.025569
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9947770
X-RAY DIFFRACTIONr_angle_other_deg1.2053.00212805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5025734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80223.363226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53215916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.21546
X-RAY DIFFRACTIONr_chiral_restr0.1240.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216428
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021202
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_it1.9261.8072948
X-RAY DIFFRACTIONr_mcbond_other1.9251.8072947
X-RAY DIFFRACTIONr_mcangle_it2.7912.6923678
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5252.252756
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 269 -
Rwork0.189 4800 -
obs--100 %

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