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

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Basic information

Entry
Database: PDB / ID: 5fjp
TitleN-acyl amino acid racemase from Amycolatopsis sp Ts-1-60: G291D F323Y I293G mutant in complex with N-acetyl naphthylalanine
ComponentsO-SUCCINYLBENZOATE SYNTHASE
KeywordsLYASE / RACEMASE / N-ACYLAMINO ACID / NAPHTHYLALANINE / ISOMERASE
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 naphthylalanine / N-succinylamino acid racemase
Similarity search - Component
Biological speciesAMYCOLATOPSIS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 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
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

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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)158,99112
Polymers157,8654
Non-polymers1,1268
Water5,495305
1
B: O-SUCCINYLBENZOATE SYNTHASE
D: O-SUCCINYLBENZOATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4966
Polymers78,9322
Non-polymers5634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-6.7 kcal/mol
Surface area25360 Å2
MethodPISA
2
A: O-SUCCINYLBENZOATE SYNTHASE
C: O-SUCCINYLBENZOATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4966
Polymers78,9322
Non-polymers5634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-16.7 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.290, 217.290, 262.220
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(0.5049, 0.8615, 0.05401), (0.8615, -0.5068, 0.03102), (0.0541, 0.03087, -0.9981)-9.461, 11.44, 83.64
2given(-0.1936, 0.4552, -0.8691), (0.4515, -0.7451, -0.4909), (-0.871, -0.4874, -0.06127)81.72, 63.96, 109
3given(0.2532, -0.416, 0.8734), (-0.4442, 0.752, 0.4869), (-0.8594, -0.5113, 0.005624)15.61, 10.31, 106.5

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Components

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


Mass: 39466.199 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-NPQ / N-acetyl naphthylalanine


Mass: 257.284 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H15NO3
#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.: 305 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS D291G F323Y I293G

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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: 3.78 Å3/Da / Density % sol: 67.5 % / Description: NONE
Crystal growpH: 8
Details: 100 MM TRIS HCL PH 8; 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: I04-1 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.58→76.44 Å / Num. obs: 74523 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.9
Reflection shellResolution: 2.58→2.65 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3 / % 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: 2.58→76.44 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.127 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20834 3755 5 %RANDOM
Rwork0.17926 ---
obs0.18074 70766 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.079 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.58→76.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10993 0 80 305 11378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01911329
X-RAY DIFFRACTIONr_bond_other_d0.0070.0211012
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.99315444
X-RAY DIFFRACTIONr_angle_other_deg1.1453.00225292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34151468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07923.273443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.844151780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9621591
X-RAY DIFFRACTIONr_chiral_restr0.0930.21792
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112819
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022400
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_it3.714.2255896
X-RAY DIFFRACTIONr_mcbond_other3.714.2255895
X-RAY DIFFRACTIONr_mcangle_it5.4866.3267356
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.384.6445433
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: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 287 -
Rwork0.351 5164 -
obs--99.93 %

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