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- PDB-5tjy: Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Myco... -

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Basic information

Entry
Database: PDB / ID: 5tjy
TitleStructure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with 2,6 Pyridine Dicarboxylic Acid and NADH
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / Lysine Biosynthesis
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase activity / diaminopimelate biosynthetic process / L-lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / cytosol
Similarity search - Function
Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
BENZOIC ACID / IMIDAZOLE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / PYRIDINE-2,6-DICARBOXYLIC ACID / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMank, N. / Arnette, K. / Klapper, V. / Chruszcz, M.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.
Authors: Pote, S. / Kachhap, S. / Mank, N.J. / Daneshian, L. / Klapper, V. / Pye, S. / Arnette, A.K. / Shimizu, L.S. / Borowski, T. / Chruszcz, M.
History
DepositionOct 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,42715
Polymers25,6821
Non-polymers1,74514
Water2,270126
1
A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,70960
Polymers102,7294
Non-polymers6,98056
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area24420 Å2
ΔGint-199 kcal/mol
Surface area34560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.421, 66.421, 249.363
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-304-

BEZ

21A-304-

BEZ

31A-304-

BEZ

41A-305-

IMD

51A-415-

HOH

61A-523-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-hydroxy-tetrahydrodipicolinate reductase / HTPA reductase


Mass: 25682.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: dapB, MRA_2798 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5U6C6, 4-hydroxy-tetrahydrodipicolinate reductase

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Non-polymers , 10 types, 140 molecules

#2: Chemical ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50 mM Ammonium Sulfate, 50 mM Bis-Tris pH 6.5, 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 13744 / % possible obs: 99.9 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.023 / Rrim(I) all: 0.105 / Χ2: 1.164 / Net I/av σ(I): 38.478 / Net I/σ(I): 7.3 / Num. measured all: 282237
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.4-2.4420.70.8130.9471100
2.44-2.4920.60.7010.9711100
2.49-2.5320.60.6570.9791100
2.53-2.5920.80.5610.9661100
2.59-2.6420.80.4820.9751100
2.64-2.720.80.4090.9821100
2.7-2.7720.60.3650.99199.9
2.77-2.8520.90.2940.9921100
2.85-2.9320.80.2780.9911100
2.93-3.0220.50.210.9941100
3.02-3.1320.80.1790.997199.7
3.13-3.2620.80.1510.998199.9
3.26-3.4120.50.120.998199.7
3.41-3.5820.80.0960.998199.9
3.58-3.8120.60.0830.9981100
3.81-4.120.70.0760.999199.7
4.1-4.5220.80.0660.9991100
4.52-5.1720.50.0520.9991100
5.17-6.5120.40.04411100
6.51-4018.30.0310.999199.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3V

1c3v


Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.696 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.19
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 663 4.9 %RANDOM
Rwork0.1456 ---
obs0.148 12914 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.3 Å2 / Biso mean: 43.662 Å2 / Biso min: 26.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.5 Å20 Å2
2--0.99 Å20 Å2
3----3.22 Å2
Refinement stepCycle: final / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 108 126 2041
Biso mean--48.53 48.46 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191964
X-RAY DIFFRACTIONr_bond_other_d0.0030.021898
X-RAY DIFFRACTIONr_angle_refined_deg1.9142.0162668
X-RAY DIFFRACTIONr_angle_other_deg1.01234350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3315248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12323.51474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36315289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.041514
X-RAY DIFFRACTIONr_chiral_restr0.1010.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212189
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02428
X-RAY DIFFRACTIONr_mcbond_it3.2094.063989
X-RAY DIFFRACTIONr_mcbond_other3.2114.058988
X-RAY DIFFRACTIONr_mcangle_it4.3126.081238
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 48 -
Rwork0.204 923 -
all-971 -
obs--99.79 %

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