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- PDB-3gc2: 1.85 Angstrom Crystal Structure of O-succinylbenzoate Synthase fr... -

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Basic information

Entry
Database: PDB / ID: 3gc2
Title1.85 Angstrom Crystal Structure of O-succinylbenzoate Synthase from Salmonella typhimurium in Complex with Succinic Acid
Componentso-succinylbenzoate synthase
KeywordsLYASE / O-succinylbenzoate synthase / Succinic Acid / idp00994 / Magnesium / Menaquinone biosynthesis / Metal-binding / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / menaquinone biosynthetic process / magnesium ion binding
Similarity search - Function
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 ...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
SUCCINIC ACID / o-succinylbenzoate synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.85 Angstrom Crystal Structure of O-succinylbenzoate Synthase from Salmonella typhimurium in Complex with Succinic Acid
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

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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)36,5438
Polymers35,9521
Non-polymers5917
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.968, 149.968, 39.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21A-567-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 35952.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: menC, STM2306 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P58486, o-succinylbenzoate synthase

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Non-polymers , 5 types, 323 molecules

#2: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M Succinic Acid,1% PEG2000MME, 0.1M HEPES (pH 7.0) , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97923 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2009 / Details: beryllium lenses
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.85→27.07 Å / Num. all: 38286 / Num. obs: 38286 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 31.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1878 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
CRANKphasing
REFMAC5.5.0044refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→27.07 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.288 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Atomic Temperature Factors Refined Individually
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1848 1915 5 %RANDOM
Rwork0.155 ---
all0.15642 36310 --
obs0.15642 36310 98.75 %-
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: 17.607 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---0.49 Å2-0 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2501 0 35 316 2852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222773
X-RAY DIFFRACTIONr_bond_other_d0.0010.021912
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9943792
X-RAY DIFFRACTIONr_angle_other_deg0.86334654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8355356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71123.252123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.50715467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2961529
X-RAY DIFFRACTIONr_chiral_restr0.0810.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_mcbond_it1.0791.51719
X-RAY DIFFRACTIONr_mcbond_other0.331.5684
X-RAY DIFFRACTIONr_mcangle_it1.81222779
X-RAY DIFFRACTIONr_scbond_it2.67431054
X-RAY DIFFRACTIONr_scangle_it4.334.51013
LS refinement shellResolution: 1.85→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 137 -
Rwork0.187 2624 -
obs-2624 99.53 %
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)
13.56530.1961-0.13241.9578-0.82161.0941-0.1228-0.1214-0.43920.0780.0559-0.32910.20480.29330.06680.14580.04660.00890.27960.03450.240658.91120.43733.0103
25.11750.8460.57713.45550.25170.9466-0.1632-0.10960.30830.05550.0892-0.2641-0.11290.22470.07390.019-0.0152-0.02170.11170.01240.057956.699731.94041.0935
31.7696-0.0939-0.12672.48330.01651.9796-0.1689-0.2154-0.11480.27210.12040.06540.09540.16940.04850.04980.04970.02380.0960.04280.019744.409821.29646.6486
43.0645-1.2913-1.0173.61931.72711.77370.0687-0.1381-0.17810.3016-0.15990.04110.3255-0.17640.09120.2275-0.00710.09790.05850.03550.115935.67481.01931.5747
51.1342-0.45830.1631.8990.34592.9247-0.12240.1334-0.2124-0.2664-0.05750.12970.2827-0.03310.17990.1416-0.00840.06450.04-0.01710.08234.299110.6616-12.3599
62.5483-0.31960.08211.75490.14431.1298-0.1298-0.1143-0.26280.1129-0.01030.03220.02110.09570.14010.03970.00770.0310.04130.02320.055940.09923.15432.0118
74.17730.5446-0.35645.01030.07151.492-0.2293-0.7813-0.45690.56060.1571-0.34090.0850.39850.07220.130.1048-0.02940.32440.13350.126257.563118.835913.2653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 35
2X-RAY DIFFRACTION2A36 - 78
3X-RAY DIFFRACTION3A79 - 117
4X-RAY DIFFRACTION4A118 - 157
5X-RAY DIFFRACTION5A158 - 229
6X-RAY DIFFRACTION6A230 - 292
7X-RAY DIFFRACTION7A293 - 320

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