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- PDB-2jla: Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydr... -

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Basic information

Entry
Database: PDB / ID: 2jla
TitleCrystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - SeMet protein
Components2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
KeywordsTRANSFERASE / MANGANESE / THIAMINE DIPHOSPHATE COFACTOR / THIAMINE PYROPHOSPHATE / MENAQUINONE BIOSYNTHESIS
Function / homology
Function and homology information


2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity / menaquinone biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Menaquinone biosynthesis protein MenD, middle domain / Middle domain of thiamine pyrophosphate / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold ...Menaquinone biosynthesis protein MenD, middle domain / Middle domain of thiamine pyrophosphate / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / THIAMINE DIPHOSPHATE / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å
AuthorsDawson, A. / Fyfe, P.K. / Hunter, W.N.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Specificity and Reactivity in Menaquinone Biosynthesis: The Structure of Escherichia Coli Mend (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase).
Authors: Dawson, A. / Fyfe, P.K. / Hunter, W.N.
History
DepositionSep 5, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
B: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
C: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
D: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,45326
Polymers248,0174
Non-polymers2,43722
Water7,116395
1
A: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
B: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,21713
Polymers124,0082
Non-polymers1,20911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-129.4 kcal/mol
Surface area38580 Å2
MethodPISA
2
C: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
D: 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,23613
Polymers124,0082
Non-polymers1,22811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-125.8 kcal/mol
Surface area38620 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27090 Å2
ΔGint-295.1 kcal/mol
Surface area69720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.830, 95.830, 463.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22B
13D
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 556
2112B1 - 556
1122C1 - 556
2122B1 - 556
1132D1 - 556
2132B1 - 556

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.998, -0.037, -0.058), (-0.032, -0.5, 0.865), (-0.061, 0.865, 0.498)70.793, -5.05, 5.607
2given(-0.996, -0.074, 0.047), (-0.078, 0.49, -0.868), (0.041, -0.869, -0.494)69.596, 12.342, 15.245
3given(0.993, 0.116, 0.009), (0.116, -0.993, 0.001), (0.009, -1)-0.045, -0.492, 19.88

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Components

#1: Protein
2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE / 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE / MENAQUINONE ...2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE / MENAQUINONE BIOSYNTHESIS PROTEIN MEND


Mass: 62004.152 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SEMET SUBSTITUTED PROTEIN / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET15BTEV_ECMEND / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3)
References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUAL GH AT N-TERMINUS FROM TAG CLEAVAGE.

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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: 2.5 Å3/Da / Density % sol: 50.7 % / Description: NONE
Crystal growpH: 8
Details: 100 MM TRIS-HCL PH 8.5, 22 % PEG 8K, 15 % GLYCEROL, 200 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97872
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.8→83 Å / Num. obs: 57944 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.6
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.4 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0046refinement
XDSdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.81→83.05 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.873 / SU B: 13.311 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2936 5.1 %RANDOM
Rwork0.169 ---
obs0.172 54880 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.69 Å20 Å2
2--1.39 Å20 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 2.81→83.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17324 0 122 395 17841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02217856
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.95324376
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89852220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99923.645812
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.936152820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.32315140
X-RAY DIFFRACTIONr_chiral_restr0.0970.22704
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113752
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3271.511092
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.658217808
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.17336764
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9794.56568
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2224tight positional0.160.05
12B2224tight positional0.160.05
21C2224tight positional0.140.05
22B2224tight positional0.140.05
31D2224tight positional0.110.05
32B2224tight positional0.110.05
11A2105medium positional0.360.5
12B2105medium positional0.360.5
21C2105medium positional0.350.5
22B2105medium positional0.350.5
31D2105medium positional0.310.5
32B2105medium positional0.310.5
11A2224tight thermal0.330.5
12B2224tight thermal0.330.5
21C2224tight thermal0.310.5
22B2224tight thermal0.310.5
31D2224tight thermal0.280.5
32B2224tight thermal0.280.5
11A2105medium thermal0.492
12B2105medium thermal0.492
21C2105medium thermal0.462
22B2105medium thermal0.462
31D2105medium thermal0.442
32B2105medium thermal0.442
LS refinement shellResolution: 2.81→2.88 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 193
Rwork0.236 3779

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