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- PDB-1r6w: Crystal structure of the K133R mutant of o-Succinylbenzoate synth... -

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Basic information

Entry
Database: PDB / ID: 1r6w
TitleCrystal structure of the K133R mutant of o-Succinylbenzoate synthase (OSBS) from Escherichia coli. Complex with SHCHC
Componentso-Succinylbenzoate Synthase
KeywordsLYASE / Enolase superfamily / TIM barrel / capping alpha+beta domain
Function / homology
Function and homology information


o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / menaquinone biosynthetic process / hydro-lyase activity / magnesium ion binding
Similarity search - Function
: / MenC, N-terminal domain / o-Succinylbenzoate synthase, MenC type1 / 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 ...: / MenC, N-terminal domain / o-Succinylbenzoate synthase, MenC type1 / 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
Chem-164 / o-succinylbenzoate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsKlenchin, V.A. / Taylor Ringia, E.A. / Gerlt, J.A. / Rayment, I.
CitationJournal: Biochemistry / Year: 2003
Title: Evolution of Enzymatic Activity in the Enolase Superfamily: Structural and Mutagenic Studies of the Mechanism of the Reaction Catalyzed by o-Succinylbenzoate Synthase from Escherichia coli
Authors: Klenchin, V.A. / Taylor Ringia, E.A. / Gerlt, J.A. / Rayment, I.
History
DepositionOct 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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

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Assembly

Deposited unit
A: o-Succinylbenzoate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0303
Polymers35,7661
Non-polymers2652
Water6,197344
1
A: o-Succinylbenzoate Synthase
hetero molecules

A: o-Succinylbenzoate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0606
Polymers71,5312
Non-polymers5294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)72.2, 82.9, 56.2
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein o-Succinylbenzoate Synthase / / E.C.4.2.1.- / OSB synthase / OSBS / 4-(2'-carboxyphenyl)-4-oxybutyric acid synthase / O-succinylbenzoic acid synthase


Mass: 35765.734 Da / Num. of mol.: 1 / Mutation: K133R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P29208, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-164 / 2-(3-CARBOXYPROPIONYL)-6-HYDROXY-CYCLOHEXA-2,4-DIENE CARBOXYLIC ACID


Mass: 240.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.11 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5
Details: The K133R mutant of OSBS was concentrated to 15 mg/ml, dialyzed against 5 mM Tris pH 8.3 containing 2 mM MgCl2, drop frozen as small pellets in liquid nitrogen and stored at -80 C. Crystals ...Details: The K133R mutant of OSBS was concentrated to 15 mg/ml, dialyzed against 5 mM Tris pH 8.3 containing 2 mM MgCl2, drop frozen as small pellets in liquid nitrogen and stored at -80 C. Crystals were grown at 20 C by small-scale batch experiments by combining 15 ml of protein solution and 15 ml of a solution containing 12-13% MePEG 5000, 100 mM sodium acetate, 60 mM MgCl2, at pH 5.5. SHCHC was included in the crystallization at a final concentration of approximately 2.5 mM., microbatch, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein11
25 mMTris-HCl11pH8.3
32 mM11MgCl2
412-13 %MePEG500011
5100 mMsodium acetate11
660 mM11pH5.5MgCl2

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.62→31 Å / Num. all: 43694 / Num. obs: 43694 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 41
Reflection shellResolution: 1.62→1.68 Å / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 17.1 / % possible all: 98.9
Reflection
*PLUS
Lowest resolution: 31.3 Å / % possible obs: 99.8 % / Redundancy: 7.05 % / Num. measured all: 307914
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fhv

1fhv


Resolution: 1.62→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.489 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20024 2190 5 %RANDOM
Rwork0.16743 ---
all0.16911 41456 --
obs0.1691 41456 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---1.38 Å20 Å2
3---1.96 Å2
Refinement stepCycle: LAST / Resolution: 1.62→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 18 344 2850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222554
X-RAY DIFFRACTIONr_bond_other_d0.0030.022374
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9733478
X-RAY DIFFRACTIONr_angle_other_deg1.23735497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735318
X-RAY DIFFRACTIONr_chiral_restr0.0940.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022845
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02498
X-RAY DIFFRACTIONr_nbd_refined0.2470.2474
X-RAY DIFFRACTIONr_nbd_other0.2530.22695
X-RAY DIFFRACTIONr_nbtor_other0.0870.21549
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.222
X-RAY DIFFRACTIONr_mcbond_it1.23621602
X-RAY DIFFRACTIONr_mcangle_it2.16232572
X-RAY DIFFRACTIONr_scbond_it3.0574.5952
X-RAY DIFFRACTIONr_scangle_it4.7326906
LS refinement shellResolution: 1.62→1.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.246 149
Rwork0.195 2994
Refinement
*PLUS
Rfactor Rfree: 0.2 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.62

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