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- PDB-2ofj: Crystal structure of the E190A mutant of o-succinylbenzoate synth... -

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Basic information

Entry
Database: PDB / ID: 2ofj
TitleCrystal structure of the E190A mutant of o-succinylbenzoate synthase from Escherichia coli
ComponentsO-succinylbenzoate synthase
KeywordsLYASE / TIM barrel
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
o-succinylbenzoate synthase
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNagatani, R.A. / Gonzalez, A. / Shoichet, B.K. / Brinen, L.S. / Babbitt, P.C.
CitationJournal: Biochemistry / Year: 2007
Title: Stability for Function Trade-Offs in the Enolase Superfamily "Catalytic Module".
Authors: Nagatani, R.A. / Gonzalez, A. / Shoichet, B.K. / Brinen, L.S. / Babbitt, P.C.
History
DepositionJan 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ... BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS BELIEVED TO BE A MONOMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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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


Theoretical massNumber of molelcules
Total (without water)142,6794
Polymers142,6794
Non-polymers00
Water3,225179
1
A: O-succinylbenzoate synthase


Theoretical massNumber of molelcules
Total (without water)35,6701
Polymers35,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: O-succinylbenzoate synthase


Theoretical massNumber of molelcules
Total (without water)35,6701
Polymers35,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: O-succinylbenzoate synthase


Theoretical massNumber of molelcules
Total (without water)35,6701
Polymers35,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: O-succinylbenzoate synthase


Theoretical massNumber of molelcules
Total (without water)35,6701
Polymers35,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.475, 77.388, 110.677
Angle α, β, γ (deg.)90.000, 90.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 320 / Label seq-ID: 4 - 323

Dom-IDEns-IDRefine codeAuth asym-IDLabel asym-ID
112BB
212AA
125CC
225AA
132DD
232CC

NCS ensembles :
ID
1
2
3
DetailsThe biological assembly is a tetramer

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Components

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


Mass: 35669.668 Da / Num. of mol.: 4 / Mutation: E190A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. (bacteria)
Species: Escherichia coli / Strain: MG1655 / Gene: menC, b2261, JW2256 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P29208, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1 M MES, 75 mM Sodium molybdate, 25% (v/v) PEG 4000, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979462 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 9, 2006 / Details: Vertical focusing mirror
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal Si(311) (horizontal focusing), asymmetric cut 12.2 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979462 Å / Relative weight: 1
ReflectionResolution: 2→43.291 Å / Num. obs: 76466 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 4.5
Reflection shell

Rmerge(I) obs: 0.018 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.053.40.31656648151.83282.8
2.05-2.113.70.42048655451.38696.8
2.11-2.173.70.61990753471.06397.1
2.17-2.243.70.81937551960.81697.3
2.24-2.313.70.81899950870.75797.5
2.31-2.393.71.21831849090.56997.6
2.39-2.483.71.41768547580.49597.7
2.48-2.583.71.91707246050.35898
2.58-2.73.72.11624543940.31398.1
2.7-2.833.731557442070.2398.2
2.83-2.983.741501140680.17398.3
2.98-3.163.75.11389137750.13397.9
3.16-3.383.66.51305935880.10398.8
3.38-3.653.67.31204033420.08298.2
3.65-43.69.41105530760.06798.3
4-4.473.610.9993727680.05898
4.47-5.163.511.4851024400.05497.3
5.16-6.323.510.5701220200.0694.5
6.32-8.943.712.8610516490.04799.5
8.94-51.783.51430658770.04493.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å43.29 Å
Translation3.5 Å43.29 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FHU

1fhu


Resolution: 2.3→43.291 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.885 / SU B: 20.367 / SU ML: 0.247 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.514 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2598 5.1 %RANDOM
Rwork0.222 ---
all0.225 48414 --
obs0.225 48414 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.243 Å2
Baniso -1Baniso -2Baniso -3
1-4.49 Å20 Å21.18 Å2
2---1.79 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9325 0 0 179 9504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229630
X-RAY DIFFRACTIONr_bond_other_d0.0070.026581
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.96813122
X-RAY DIFFRACTIONr_angle_other_deg0.889315980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80151202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7623.576439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.124151603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.981593
X-RAY DIFFRACTIONr_chiral_restr0.160.21481
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210760
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021937
X-RAY DIFFRACTIONr_nbd_refined0.2170.22120
X-RAY DIFFRACTIONr_nbd_other0.2070.27051
X-RAY DIFFRACTIONr_nbtor_refined0.1740.24544
X-RAY DIFFRACTIONr_nbtor_other0.0850.25380
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2374
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.27
X-RAY DIFFRACTIONr_mcbond_it0.7661.57720
X-RAY DIFFRACTIONr_mcbond_other0.0931.52404
X-RAY DIFFRACTIONr_mcangle_it0.76129693
X-RAY DIFFRACTIONr_scbond_it1.30134194
X-RAY DIFFRACTIONr_scangle_it1.7964.53429
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1769TIGHT POSITIONAL0.110.2
1B2253MEDIUM POSITIONAL0.61
1B1769TIGHT THERMAL0.492
1B2253MEDIUM THERMAL0.685
2C1723MEDIUM POSITIONAL0.351
2C2135LOOSE POSITIONAL0.745
2C1723MEDIUM THERMAL4.945
2C2135LOOSE THERMAL5.0210
3D1717TIGHT POSITIONAL0.120.2
3D2138MEDIUM POSITIONAL0.641
3D1717TIGHT THERMAL0.512
3D2138MEDIUM THERMAL0.725
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 190 -
Rwork0.25 3554 -
obs-3744 97.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.54910.19330.64244.15920.77875.32550.03090.0493-0.03080.0288-0.0324-0.1604-0.22010.210.0015-0.0341-0.0277-0.0629-0.10740.0342-0.1212.026-24.73253.494
21.0150.6033-0.36661.605-0.421.6303-0.02980.020.0078-0.08620.0702-0.05460.09650.0476-0.0404-0.0466-0.0009-0.0434-0.0636-0.0092-0.09141.162-4.09835.72
31.4519-0.4860.23823.3120.39292.9787-0.0779-0.02810.0067-0.0285-0.0214-0.06190.10510.14910.09940.00170.0384-0.0112-0.08370.0287-0.09772.036-13.5131.76
41.036-0.68250.28841.5571-0.20411.38860.00230.03090.00610.11420.0616-0.0403-0.11130.0678-0.0639-0.0414-0.0008-0.0461-0.06470.0023-0.07541.168-34.11919.639
55.1485-2.09440.680110.35370.23892.6199-0.32820.7796-0.2157-0.05650.74880.3170.04920.1732-0.4206-0.1951-0.0916-0.10320.2591-0.0134-0.048726.713-10.374-4.208
63.12950.59231.75440.97790.48013.59710.15470.0929-0.01860.1671-0.09010.08630.1207-0.0773-0.0646-0.1759-0.0076-0.05910.0385-0.01150.032639.8850.08617.163
73.70240.5292-0.96956.57030.91692.584-0.19-0.71540.10570.14940.4290.2039-0.05010.1215-0.239-0.19630.0758-0.02620.1775-0.0255-0.072326.397-28.04459.634
83.244-0.7491-1.62071.09810.22883.14420.0557-0.0067-0.0382-0.21610.00290.0923-0.052-0.1199-0.0587-0.2125-0.0118-0.0394-0.01470.0025-0.016339.679-38.21538.194
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA107 - 211110 - 214
22AA1 - 1064 - 109
32AA212 - 320215 - 323
43BB107 - 211110 - 214
54BB1 - 1064 - 109
64BB212 - 320215 - 323
75CC107 - 211110 - 214
86CC1 - 1064 - 109
96CC212 - 320215 - 323
107DD107 - 211110 - 214
118DD1 - 1064 - 109
128DD212 - 320215 - 323

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