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- PDB-7s8w: Amycolatopsis sp. T-1-60 N-succinylamino acid racemase/o-succinyl... -

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Basic information

Entry
Database: PDB / ID: 7s8w
TitleAmycolatopsis sp. T-1-60 N-succinylamino acid racemase/o-succinylbenzoate synthase R266Q mutant in complex with N-succinylphenylglycine
ComponentsN-succinylamino acid racemase/O-succinylbenzoate synthase
KeywordsISOMERASE / Complex / racemase / dehydratase / mutant
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, N-terminal / Enolase-like, C-terminal domain superfamily
Similarity search - Domain/homology
N-succinyl-L-phenylglycine / N-succinylamino acid racemase
Similarity search - Component
Biological speciesAmycolatopsis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTruong, D.P. / Rousseau, S. / Sacchettini, J.C. / Glasner, M.E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1253975 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM124409 United States
Welch FoundationA-1991-20190330 United States
Welch FoundationA-0015 United States
Citation
Journal: Biochemistry / Year: 2021
Title: Second-Shell Amino Acid R266 Helps Determine N -Succinylamino Acid Racemase Reaction Specificity in Promiscuous N -Succinylamino Acid Racemase/ o -Succinylbenzoate Synthase Enzymes.
Authors: Truong, D.P. / Rousseau, S. / Machala, B.W. / Huddleston, J.P. / Zhu, M. / Hull, K.G. / Romo, D. / Raushel, F.M. / Sacchettini, J.C. / Glasner, M.E.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionSep 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 29, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-succinylamino acid racemase/O-succinylbenzoate synthase
B: N-succinylamino acid racemase/O-succinylbenzoate synthase
C: N-succinylamino acid racemase/O-succinylbenzoate synthase
D: N-succinylamino acid racemase/O-succinylbenzoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,01713
Polymers157,6774
Non-polymers1,3409
Water2,360131
1
A: N-succinylamino acid racemase/O-succinylbenzoate synthase
B: N-succinylamino acid racemase/O-succinylbenzoate synthase
C: N-succinylamino acid racemase/O-succinylbenzoate synthase
D: N-succinylamino acid racemase/O-succinylbenzoate synthase
hetero molecules

A: N-succinylamino acid racemase/O-succinylbenzoate synthase
B: N-succinylamino acid racemase/O-succinylbenzoate synthase
C: N-succinylamino acid racemase/O-succinylbenzoate synthase
D: N-succinylamino acid racemase/O-succinylbenzoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,03526
Polymers315,3548
Non-polymers2,68118
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_767-x+8/3,-x+y+4/3,-z+7/31
Unit cell
Length a, b, c (Å)213.742, 213.742, 253.077
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 324 or resid 326 through 367))
d_2ens_1(chain "B" and (resid 1 through 324 or resid 326 through 367))
d_3ens_1(chain "C" and (resid 1 through 324 or resid 326 through 367))
d_4ens_1(chain "D" and resid 1 through 367)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METTYRA1 - 324
d_12ens_1THRGLYA326 - 367
d_21ens_1METTYRD1 - 324
d_22ens_1THRGLYD326 - 367
d_31ens_1METTYRF1 - 324
d_32ens_1THRGLYF326 - 367
d_41ens_1METGLYM1 - 366

NCS oper:
IDCodeMatrixVector
1given(0.518639823626, 0.854598302078, -0.0259706648943), (0.854409846869, -0.519168551465, -0.0211619645414), (-0.0315681314395, -0.0112141542581, -0.999438690377)-105.652585675, 207.944383999, 598.28832049
2given(0.233317164249, -0.418885915152, 0.877552101561), (-0.436934220081, 0.7610623848, 0.479450241176), (-0.868706848245, -0.495296513746, -0.00545667320163)-46.3127301855, -20.2949080371, 543.231271665
3given(-0.231099438475, 0.462946969728, 0.855729602594), (0.454934714246, -0.726044962598, 0.515648250321), (0.860015962241, 0.508467123329, -0.04282206422)-161.683770644, 158.760976116, 60.2221085425

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Components

#1: Protein
N-succinylamino acid racemase/O-succinylbenzoate synthase / OSB synthase / OSBS / 4-(2'-carboxyphenyl)-4-oxybutyric acid synthase / o-succinylbenzoic acid synthase


Mass: 39419.203 Da / Num. of mol.: 4 / Mutation: R266Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis sp. (bacteria) / Gene: Aaar, menC / Production host: Escherichia coli (E. coli) / References: UniProt: Q44244, o-succinylbenzoate synthase
#2: Chemical
ChemComp-8JI / N-succinyl-L-phenylglycine


Mass: 251.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H13NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 28% PEG 4000 0.1 M Tris (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 49028 / % possible obs: 99.89 % / Redundancy: 6.8 % / Biso Wilson estimate: 66 Å2 / Rrim(I) all: 0.185 / Net I/σ(I): 8.64
Reflection shellResolution: 2.93→3 Å / Redundancy: 2.1 % / Num. unique obs: 4865 / CC1/2: 0.759

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SBC-Collect1.18.2_3874data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SJB

1sjb


Resolution: 2.9→49.8 Å / SU ML: 0.3254 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.5588
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2152 1996 4.07 %
Rwork0.1701 47015 -
obs0.172 49011 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.55 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11055 0 92 131 11278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008411365
X-RAY DIFFRACTIONf_angle_d1.127715468
X-RAY DIFFRACTIONf_chiral_restr0.07081793
X-RAY DIFFRACTIONf_plane_restr0.00772024
X-RAY DIFFRACTIONf_dihedral_angle_d21.98194159
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.607264948824
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.604049348201
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.604458990459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.32251400.26693323X-RAY DIFFRACTION100
2.98-3.060.29061460.23723334X-RAY DIFFRACTION100
3.06-3.150.2921450.22263331X-RAY DIFFRACTION99.97
3.15-3.250.27351330.20913351X-RAY DIFFRACTION99.97
3.25-3.360.27371420.20873308X-RAY DIFFRACTION100
3.36-3.50.23021420.20093355X-RAY DIFFRACTION100
3.5-3.660.21331450.17643329X-RAY DIFFRACTION99.97
3.66-3.850.19471470.16743353X-RAY DIFFRACTION100
3.85-4.090.22331400.16493339X-RAY DIFFRACTION100
4.09-4.410.19811420.15463361X-RAY DIFFRACTION100
4.41-4.850.17241440.13813371X-RAY DIFFRACTION99.91
4.85-5.550.21191480.15493373X-RAY DIFFRACTION99.94
5.55-6.990.19991340.16783402X-RAY DIFFRACTION99.89
6.99-49.80.18781480.14323485X-RAY DIFFRACTION99.34

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