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- PDB-4jdy: Crystal structure of Rv2606c -

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Basic information

Entry
Database: PDB / ID: 4jdy
TitleCrystal structure of Rv2606c
ComponentsPyridoxal biosynthesis lyase PdxS
KeywordsLYASE / (beta/alpha)8-barrel
Function / homology
Function and homology information


amine-lyase activity / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / amino acid metabolic process / plasma membrane
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PdxS / Pyridoxal 5'-phosphate synthase subunit PdxS
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKim, S. / Kim, K.-J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystal structure of Mycobacterium tuberculosis Rv2606c: a pyridoxal biosynthesis lyase.
Authors: Kim, S. / Kim, K.J.
History
DepositionFeb 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8356
Polymers83,5593
Non-polymers2763
Water8,017445
1
A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
hetero molecules

A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
hetero molecules

A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
hetero molecules

A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,34224
Polymers334,23712
Non-polymers1,10512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area39650 Å2
ΔGint-173 kcal/mol
Surface area103670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.752, 126.080, 180.816
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Pyridoxal biosynthesis lyase PdxS


Mass: 27853.072 Da / Num. of mol.: 3 / Fragment: UNP residues 11-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pdxS, Rv2606c, MT2681, MTCY1A10.27 / Plasmid: pProEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P60796, UniProt: P9WII9*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.78 Å3/Da / Density % sol: 67.43 % / Mosaicity: 0.28 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: PEG 8000, CAPS, NaCl, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionRedundancy: 5.3 % / Av σ(I) over netI: 20.19 / Number: 609007 / Rmerge(I) obs: 0.072 / Χ2: 0.98 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 115287 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.885099.610.0441.5476.3
3.083.8899.710.0521.2836.4
2.693.0899.410.0731.0595.8
2.442.6999.410.0950.9795.7
2.272.4499.410.1190.9075.4
2.132.2799.210.1470.8345.3
2.032.1399.310.1890.7915.1
1.942.0398.910.2380.6834.7
1.861.9498.410.2910.5854.2
1.81.869710.3280.5493.8
ReflectionResolution: 1.8→50 Å / Num. obs: 115287 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.072 / Χ2: 0.978 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.863.80.328112280.549197
1.86-1.944.20.291113170.585198.4
1.94-2.034.70.238114330.683198.9
2.03-2.135.10.189114650.791199.3
2.13-2.275.30.147114910.834199.2
2.27-2.445.40.119115020.907199.4
2.44-2.695.70.095115720.979199.4
2.69-3.085.80.073116001.059199.4
3.08-3.886.40.052116821.283199.7
3.88-506.30.044119971.547199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ISS

2iss


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1898 / WRfactor Rwork: 0.1651 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8912 / SU B: 1.967 / SU ML: 0.061 / SU R Cruickshank DPI: 0.092 / SU Rfree: 0.0929 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 5765 5 %RANDOM
Rwork0.1829 ---
obs0.1843 115269 99 %-
all-153419 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.74 Å2 / Biso mean: 23.2308 Å2 / Biso min: 6.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5841 0 18 445 6304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0225943
X-RAY DIFFRACTIONr_angle_refined_deg2.2021.9688037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27723.421228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13815996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9871548
X-RAY DIFFRACTIONr_chiral_restr0.1810.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214425
X-RAY DIFFRACTIONr_mcbond_it1.6051.53915
X-RAY DIFFRACTIONr_mcangle_it2.7126255
X-RAY DIFFRACTIONr_scbond_it4.02432028
X-RAY DIFFRACTIONr_scangle_it6.2494.51782
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 396 -
Rwork0.278 7803 -
all-8199 -
obs--95.98 %

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