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- PDB-5erx: Crystal Structure of APO MenD from M. tuberculosis - I222 -

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Basic information

Entry
Database: PDB / ID: 5erx
TitleCrystal Structure of APO MenD from M. tuberculosis - I222
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.729 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: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _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 ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase


Theoretical massNumber of molelcules
Total (without water)60,0691
Polymers60,0691
Non-polymers00
Water5,080282
1
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase


Theoretical massNumber of molelcules
Total (without water)240,2764
Polymers240,2764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area15140 Å2
ΔGint-73 kcal/mol
Surface area71880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.059, 105.502, 120.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

21A-647-

HOH

31A-666-

HOH

41A-785-

HOH

51A-840-

HOH

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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.: 1
Source method: isolated from a genetically manipulated source
Details: The protein was expressed as a his-tag construct and contains a N-terminal poly-histidine tag sequence not seen in the crystal structure. The protein has been numbered as it would be in the ...Details: The protein was expressed as a his-tag construct and contains a N-terminal poly-histidine tag sequence not seen in the crystal structure. The protein has been numbered as it would be in the non-tagged protein so as to match the deposited biological sequence (e.g. start 1 = residue 1 in sequence database).
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


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 277 K / Method: batch mode
Details: Crystals grew in the fridge in the purification buffer.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.729→19.661 Å / Num. obs: 62875 / % possible obs: 94.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 26.98 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.023 / Net I/σ(I): 22.6 / Num. measured all: 318157
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.73-1.764.10.7242.21129827720.3480.38577.7
8.98-19.664.60.011110.9219747910.00690.1

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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: 1.729→19.661 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 3207 5.1 %
Rwork0.2287 59634 -
obs0.2303 62841 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.36 Å2 / Biso mean: 40.9003 Å2 / Biso min: 17.69 Å2
Refinement stepCycle: final / Resolution: 1.729→19.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 0 282 3974
Biso mean---43.84 -
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053813
X-RAY DIFFRACTIONf_angle_d0.6715232
X-RAY DIFFRACTIONf_chiral_restr0.047626
X-RAY DIFFRACTIONf_plane_restr0.005697
X-RAY DIFFRACTIONf_dihedral_angle_d13.7762313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7289-1.75470.48881080.52011991209973
1.7547-1.78210.42871270.44092500262792
1.7821-1.81130.46671240.40352501262592
1.8113-1.84250.38051460.3632522266893
1.8425-1.8760.40511430.35272502264593
1.876-1.9120.34941210.33572560268193
1.912-1.9510.35261170.32012564268194
1.951-1.99340.3331610.29642538269994
1.9934-2.03970.36541510.27752538268994
2.0397-2.09070.30721250.26732602272795
2.0907-2.14710.27361520.27142595274795
2.1471-2.21020.31311270.24782602272995
2.2102-2.28150.29631530.2482579273295
2.2815-2.36290.27641470.24922637278496
2.3629-2.45730.27531460.24512622276896
2.4573-2.56890.31081570.23542626278396
2.5689-2.7040.26871450.23592672281797
2.704-2.8730.27041430.22832657280097
2.873-3.0940.24741510.21592706285798
3.094-3.40390.25661360.20932717285398
3.4039-3.89320.21721300.19562746287698
3.8932-4.89250.2031510.16872762291398
4.8925-19.66250.18971460.19662895304199

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