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- PDB-4a6g: N-acyl amino acid racemase from Amycalotopsis sp. Ts-1-60: G291D-... -

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Basic information

Entry
Database: PDB / ID: 4a6g
TitleN-acyl amino acid racemase from Amycalotopsis sp. Ts-1-60: G291D- F323Y mutant in complex with N-acetyl methionine
ComponentsN-ACYLAMINO ACID RACEMASE
KeywordsLYASE / BIOCATALYSIS
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-ACETYLMETHIONINE / N-succinylamino acid racemase
Similarity search - Component
Biological speciesAMYCOLATOPSIS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsBaxter, S. / Royer, S. / Grogan, G. / Holt-Tiffin, K.E. / Taylor, I.N. / Fotheringham, I.G. / Campopiano, D.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: An Improved Racemase/Acylase Biotransformation for the Preparation of Enantiomerically Pure Amino Acids.
Authors: Baxter, S. / Royer, S. / Grogan, G. / Brown, F. / Holt-Tiffin, K.E. / Taylor, I.N. / Fotheringham, I.G. / Campopiano, D.J.
History
DepositionNov 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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)158,95112
Polymers158,0894
Non-polymers8628
Water4,774265
1
A: N-ACYLAMINO ACID RACEMASE
C: N-ACYLAMINO ACID RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4766
Polymers79,0452
Non-polymers4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-18.9 kcal/mol
Surface area25480 Å2
MethodPISA
2
B: N-ACYLAMINO ACID RACEMASE
D: N-ACYLAMINO ACID RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4766
Polymers79,0452
Non-polymers4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-9.3 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.710, 216.710, 261.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 368
2114B1 - 368
3114C1 - 368
4114D1 - 368

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.508797, -0.860006, -0.038915), (-0.859897, -0.509859, 0.024903), (-0.041258, 0.020793, -0.998932)-8.59442, -11.28431, -84.4511
3given(-0.200334, -0.44535, 0.872657), (-0.441462, -0.754131, -0.486207), (0.87463, -0.482649, -0.045527)82.81653, -63.77607, -107.96628
4given(0.25328, 0.404444, -0.878791), (0.450833, 0.754387, 0.477126), (0.85592, -0.517035, 0.008734)15.17345, -10.82645, -106.26589

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Components

#1: Protein
N-ACYLAMINO ACID RACEMASE / O-SUCCINYL BENZOATE SYNTHASE


Mass: 39522.305 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMYCOLATOPSIS SP. (bacteria) / Strain: TS-1-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44244, o-succinylbenzoate synthase
#2: Chemical
ChemComp-AME / N-ACETYLMETHIONINE


Type: L-peptide NH3 amino terminus / Mass: 191.248 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13NO3S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 265 / 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: 3.74 Å3/Da / Density % sol: 67.2 % / Description: NONE
Crystal growpH: 8
Details: PROTEIN CONCENTRATION OF 8 MG ML-1 THAT HAD BEEN INCUBATED PREVIOUSLY WITH 10 MM N-ACETYL METHIONINE. CRYSTAL DROPS CONTAINED 100 MM TRIS-HCL (PH 8.0) 15% PEG 4K, 800 MM NA FORMATE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.71→88.31 Å / Num. obs: 60693 / % possible obs: 100 % / Observed criterion σ(I): 4.8 / Redundancy: 10.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.6
Reflection shellResolution: 2.71→2.79 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SJA

1sja


Resolution: 2.71→88.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.097 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21012 3226 5 %RANDOM
Rwork0.15535 ---
obs0.15816 60693 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.754 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.71→88.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10897 0 52 265 11214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02211165
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0971.9915227
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89151465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30423.01412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.631151730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1851586
X-RAY DIFFRACTIONr_chiral_restr0.1380.21801
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218378
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 2683 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.370.5
2Bmedium positional0.340.5
3Cmedium positional0.370.5
4Dmedium positional0.340.5
1Amedium thermal8.622
2Bmedium thermal5.122
3Cmedium thermal6.272
4Dmedium thermal5.462
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 241 -
Rwork0.258 4296 -
obs--100 %

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