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- PDB-5ery: Crystal Structure of APO MenD from M. tuberculosis - P212121 -

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Basic information

Entry
Database: PDB / ID: 5ery
TitleCrystal Structure of APO MenD from M. tuberculosis - P212121
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / menaquinone biosynthesis / MenD / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase / thiamin-diphosphate dependent enzyme / pyruvate oxidase family
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 / plasma membrane
Similarity search - Function
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 / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsJohnston, J.M. / Jirgis, E.N.M. / Bashiri, G. / Bulloch, E.M.M. / Baker, E.N.
CitationJournal: Structure / Year: 2016
Title: Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
Authors: Jirgis, E.N. / Bashiri, G. / Bulloch, E.M. / Johnston, J.M. / Baker, E.N.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase


Theoretical massNumber of molelcules
Total (without water)240,2764
Polymers240,2764
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14930 Å2
ΔGint-59 kcal/mol
Surface area70940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.405, 137.283, 164.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / SEPHCHC synthase / Menaquinone biosynthesis protein MenD


Mass: 60068.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Protein contains an N-terminal histidine tag from cloning. This tag is not seen in the crystal structure. The protein is numbered as it would be in the native sequence.
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: menD, Rv0555 / Production host: Mycobacterium smegmatis (bacteria)
References: UniProt: P9WK11, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 8% PEG 6000, 0.1 M HEPES pH 7.5, and 3% 1,6-diaminohexane

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.25→164.93 Å / Num. obs: 107547 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 46.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.036 / Net I/σ(I): 14.9 / Num. measured all: 798333 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.25-2.297.51.4941.53955352710.540.584100
12.32-164.936.10.03541.745917530.9980.01598.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→49.703 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 5379 5.01 %
Rwork0.2118 102051 -
obs0.2136 107430 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.97 Å2 / Biso mean: 55.9777 Å2 / Biso min: 23.46 Å2
Refinement stepCycle: final / Resolution: 2.25→49.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14371 0 0 311 14682
Biso mean---45.46 -
Num. residues----1971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714775
X-RAY DIFFRACTIONf_angle_d0.9620261
X-RAY DIFFRACTIONf_chiral_restr0.0562439
X-RAY DIFFRACTIONf_plane_restr0.0082685
X-RAY DIFFRACTIONf_dihedral_angle_d16.4378947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.27560.35631780.338233433521100
2.2756-2.30230.38881750.321533853560100
2.3023-2.33040.31461760.318233473523100
2.3304-2.35990.36531750.307433873562100
2.3599-2.3910.34661860.287333613547100
2.391-2.42370.33621910.2733453536100
2.4237-2.45840.31521780.272533713549100
2.4584-2.4950.32731810.262133853566100
2.495-2.5340.35871670.265233703537100
2.534-2.57560.34351870.254733393526100
2.5756-2.620.28781730.250733943567100
2.62-2.66760.32781690.245933833552100
2.6676-2.71890.28421650.248833883553100
2.7189-2.77440.30021640.24533923556100
2.7744-2.83470.30321700.254334143584100
2.8347-2.90070.29771450.252734043549100
2.9007-2.97320.29021740.240533863560100
2.9732-3.05360.2721900.239533813571100
3.0536-3.14340.27771790.224633973576100
3.1434-3.24490.28531920.227533693561100
3.2449-3.36080.27011720.225734193591100
3.3608-3.49540.24041870.213433953582100
3.4954-3.65440.22931690.193934243593100
3.6544-3.8470.21291810.195534243605100
3.847-4.08790.20511640.192934243588100
4.0879-4.40340.21861920.173434273619100
4.4034-4.84610.19221830.16834513634100
4.8461-5.54660.22062040.181534463650100
5.5466-6.9850.22552090.192134893698100
6.985-49.71460.18292030.17833611381499

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