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- PDB-2ozt: Crystal structure of O-succinylbenzoate synthase from Thermosynec... -

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Basic information

Entry
Database: PDB / ID: 2ozt
TitleCrystal structure of O-succinylbenzoate synthase from Thermosynechococcus elongatus BP-1
ComponentsTlr1174 protein
KeywordsLYASE / STRUCTURAL GENOMICS / O-succinylbenzoate synthase / PSI / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / phylloquinone biosynthetic process / menaquinone biosynthetic process / 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
PHOSPHATE ION / o-succinylbenzoate synthase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.42 Å
AuthorsMalashkevich, V.N. / Bonanno, J. / Toro, R. / Sauder, J.M. / Schwinn, K.D. / Bain, K.T. / Adams, J.M. / Reyes, C. / Rooney, I. / Gheyi, T. ...Malashkevich, V.N. / Bonanno, J. / Toro, R. / Sauder, J.M. / Schwinn, K.D. / Bain, K.T. / Adams, J.M. / Reyes, C. / Rooney, I. / Gheyi, T. / Wasserman, S.R. / Emtage, S. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.
Authors: Odokonyero, D. / Sakai, A. / Patskovsky, Y. / Malashkevich, V.N. / Fedorov, A.A. / Bonanno, J.B. / Fedorov, E.V. / Toro, R. / Agarwal, R. / Wang, C. / Ozerova, N.D. / Yew, W.S. / Sauder, J.M. ...Authors: Odokonyero, D. / Sakai, A. / Patskovsky, Y. / Malashkevich, V.N. / Fedorov, A.A. / Bonanno, J.B. / Fedorov, E.V. / Toro, R. / Agarwal, R. / Wang, C. / Ozerova, N.D. / Yew, W.S. / Sauder, J.M. / Swaminathan, S. / Burley, S.K. / Almo, S.C. / Glasner, M.E.
History
DepositionFeb 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 11, 2014Group: Database references
Revision 1.4Aug 13, 2014Group: Database references
Revision 1.5Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.7Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.8Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tlr1174 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8344
Polymers37,6211
Non-polymers2133
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.641, 113.498, 148.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tlr1174 protein


Mass: 37621.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: BP-1 / Gene: tlr1174 / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DJP8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% PEG8000, 0.1M phosphate-citrate, pH 4.2, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97969 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97969 Å / Relative weight: 1
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 10.7 / Number: 776620 / Rmerge(I) obs: 0.058 / Χ2: 1.46 / D res high: 1.42 Å / D res low: 20 Å / Num. obs: 116450 / % possible obs: 95.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.852099.310.0392.3397.6
3.063.8510010.0442.3847.7
2.673.0610010.0522.1897.6
2.432.6710010.0581.9947.3
2.252.4399.810.0651.8867
2.122.2599.210.0691.8146.7
2.012.1297.710.0781.626.6
1.932.0196.510.0911.4466.5
1.851.9395.610.1121.3886.6
1.791.8595.610.1351.2266.6
1.731.7994.710.1631.1866.6
1.681.7395.210.1991.0996.6
1.641.6894.510.2351.0466.7
1.61.6494.710.2790.9876.6
1.561.694.910.3120.9556.5
1.531.569410.3560.9266.3
1.51.5392.610.4170.9036.1
1.471.590.210.4650.8655.9
1.441.4786.210.5920.8225.7
1.421.4482.210.6270.8175.6
ReflectionResolution: 1.42→20 Å / Num. obs: 116450 / % possible obs: 95.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.058 / Χ2: 1.462 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.42-1.445.60.62750130.817182.2
1.44-1.475.70.59253420.822186.2
1.47-1.55.90.46554310.865190.2
1.5-1.536.10.41756810.903192.6
1.53-1.566.30.35657410.926194
1.56-1.66.50.31258040.955194.9
1.6-1.646.60.27957940.987194.7
1.64-1.686.70.23557841.046194.5
1.68-1.736.60.19958421.099195.2
1.73-1.796.60.16358061.186194.7
1.79-1.856.60.13558011.226195.6
1.85-1.936.60.11258911.388195.6
1.93-2.016.50.09159131.446196.5
2.01-2.126.60.07859431.62197.7
2.12-2.256.70.06960751.814199.2
2.25-2.4370.06561371.886199.8
2.43-2.677.30.05861161.9941100
2.67-3.067.60.05261322.1891100
3.06-3.857.70.04460972.3841100
3.85-207.60.03961072.339199.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0028refinement
SHELXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
MAR345CCDdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.42→19.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.247 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20706 3115 5.1 %RANDOM
Rwork0.17755 ---
obs0.17909 58225 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.42→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 11 382 2948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222672
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9443662
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6265326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51223.089123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3115409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0211523
X-RAY DIFFRACTIONr_chiral_restr0.1010.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022083
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21207
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21819
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0151.51617
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75822597
X-RAY DIFFRACTIONr_scbond_it2.50931154
X-RAY DIFFRACTIONr_scangle_it3.9624.51064
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 168 -
Rwork0.338 3591 -
obs--81.36 %

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