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- PDB-5fju: N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: Q26A M... -

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Basic information

Entry
Database: PDB / ID: 5fju
TitleN-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: Q26A M50I G291D F323Y mutant in complex with N-acetyl phenylalanine
ComponentsO-SUCCINYLBENZOATE SYNTHASE
KeywordsISOMERASE / RACEMASE / N-ACYL AMINO ACID
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-acetyl-L-phenylalanine / N-succinylamino acid racemase
Similarity search - Component
Biological speciesAMYCOLATOPSIS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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 13, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: O-SUCCINYLBENZOATE SYNTHASE
B: O-SUCCINYLBENZOATE SYNTHASE
C: O-SUCCINYLBENZOATE SYNTHASE
D: O-SUCCINYLBENZOATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,54416
Polymers157,7894
Non-polymers1,75512
Water8,449469
1
A: O-SUCCINYLBENZOATE SYNTHASE
B: O-SUCCINYLBENZOATE SYNTHASE
C: O-SUCCINYLBENZOATE SYNTHASE
D: O-SUCCINYLBENZOATE SYNTHASE
hetero molecules

A: O-SUCCINYLBENZOATE SYNTHASE
B: O-SUCCINYLBENZOATE SYNTHASE
C: O-SUCCINYLBENZOATE SYNTHASE
D: O-SUCCINYLBENZOATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,08832
Polymers315,5788
Non-polymers3,51024
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area29460 Å2
ΔGint-137.5 kcal/mol
Surface area90450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.900, 216.900, 261.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.5115, 0.8586, 0.03448), (0.8586, -0.5123, 0.02076), (0.03549, 0.01899, -0.9992)-8.192, 11.21, 84.95
2given(-0.2036, 0.4417, -0.8737), (0.4353, -0.7585, -0.4849), (-0.8769, -0.4791, -0.03785)83.51, 63.78, 107.7
3given(0.2526, -0.4035, 0.8794), (-0.4513, 0.7548, 0.476), (-0.8559, -0.5171, 0.008596)15.18, 10.84, 106.3

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Components

#1: Protein
O-SUCCINYLBENZOATE SYNTHASE / OSB SYNTHASE / OSBS / "4-(2-CARBOXYPHENYL)-4-OXYBUTYRIC ACID SYNTHASE" / O-SUCCINYLBENZOIC ACID ...OSB SYNTHASE / OSBS / "4-(2-CARBOXYPHENYL)-4-OXYBUTYRIC ACID SYNTHASE" / O-SUCCINYLBENZOIC ACID SYNTHASE / N-ACYL AMINO ACID RACEMASE


Mass: 39447.219 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 / Plasmid: PET-20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44244, o-succinylbenzoate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-5CR / N-acetyl-L-phenylalanine


Type: L-peptide linking / Mass: 207.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H13NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS Q26A M50I D291G F323Y

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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: 3.76 Å3/Da / Density % sol: 67.3 % / Description: NONE
Crystal growpH: 8
Details: 100 MM TRIS HCL PH 8.0; 15% (W/V) 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: I03 / Wavelength: 0.97623
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.52→107.35 Å / Num. obs: 79550 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 10 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A6G

4a6g


Resolution: 2.52→107.35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.967 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 3783 4.8 %RANDOM
Rwork0.15635 ---
obs0.158 75765 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.372 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0.52 Å20 Å2
2---1.04 Å20 Å2
3---3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.52→107.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10968 0 124 469 11561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01911366
X-RAY DIFFRACTIONr_bond_other_d0.0090.0211078
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.99515491
X-RAY DIFFRACTIONr_angle_other_deg1.4883.00325438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02551465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.37523.228443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.223151779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9361592
X-RAY DIFFRACTIONr_chiral_restr0.1020.21805
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112839
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022409
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_it3.7854.475896
X-RAY DIFFRACTIONr_mcbond_other3.7814.475895
X-RAY DIFFRACTIONr_mcangle_it5.266.6967349
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3265.0355470
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: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 238 -
Rwork0.27 5618 -
obs--99.95 %

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