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- PDB-5ugv: DapB from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 5ugv
TitleDapB from Mycobacterium tuberculosis
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / lysine biosynthesis / DapB
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 / NADH binding / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NADPH binding / peptidoglycan-based cell wall / NAD binding / NADP binding ...4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / NADH binding / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NADPH binding / peptidoglycan-based cell wall / NAD binding / NADP binding / plasma membrane / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPote, S.P. / Mank, N. / 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
DepositionJan 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate reductase
B: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7707
Polymers57,0472
Non-polymers1,7235
Water1,63991
1
A: 4-hydroxy-tetrahydrodipicolinate reductase
B: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
B: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,54014
Polymers114,0934
Non-polymers3,44710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area15250 Å2
ΔGint-101 kcal/mol
Surface area38080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.507, 88.566, 77.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 0 - 242 / Label seq-ID: 25 - 267

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 28523.287 Da / Num. of mol.: 2
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 / Plasmid: pJ411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5U6C6, UniProt: P9WP23*PLUS, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate monohydrate, 0.1 M tris pH 8.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. obs: 27944 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.036 / Rrim(I) all: 0.074 / Rsym value: 0.06 / Net I/σ(I): 29.6
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1353 / CC1/2: 0.776 / Rpim(I) all: 0.389 / Rrim(I) all: 0.798 / Rsym value: 0.652 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YL6

1yl6


Resolution: 2.25→40 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19982 1400 5 %RANDOM
Rwork0.16496 ---
obs0.16679 26507 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.517 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--2.41 Å2-0 Å2
3----3.51 Å2
Refinement stepCycle: 1 / Resolution: 2.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 102 91 3772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193753
X-RAY DIFFRACTIONr_bond_other_d00.023619
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9965127
X-RAY DIFFRACTIONr_angle_other_deg3.76638305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6725487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08623.714140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42815551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8771524
X-RAY DIFFRACTIONr_chiral_restr0.1090.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214199
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02796
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_it2.353.4741954
X-RAY DIFFRACTIONr_mcbond_other2.3393.4741953
X-RAY DIFFRACTIONr_mcangle_it3.6635.2012439
X-RAY DIFFRACTIONr_mcangle_other3.6655.2032440
X-RAY DIFFRACTIONr_scbond_it3.6174.1311798
X-RAY DIFFRACTIONr_scbond_other3.6154.1311798
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6966.0122689
X-RAY DIFFRACTIONr_long_range_B_refined7.60728.8763779
X-RAY DIFFRACTIONr_long_range_B_other7.60628.883780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27452 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.254→2.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 89 -
Rwork0.25 1787 -
obs--89.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9465-0.2043-0.52092.1589-1.09023.4958-0.08790.1360.0320.1276-0.0813-0.0896-0.13440.45510.16910.0443-0.0617-0.05410.23960.03550.089862.93262.6363.769
22.5432.09870.32133.58652.53924.08780.14220.0939-0.16070.2760.1198-0.38910.07010.2175-0.2620.14520.0715-0.09350.084-0.02960.224259.9349.19927.362
31.97650.6643-0.60274.25090.99461.2530.155-0.0081-0.32060.52690.0353-0.66420.05810.1477-0.19040.17230.0653-0.15420.0736-0.05760.285957.21940.9929.425
41.34831.6741-1.52552.4283-1.72243.72020.04530.14420.07780.26330.15470.0115-0.34660.1298-0.20.2177-0.0351-0.02940.17380.00210.182853.82960.81216.104
52.5641-0.14860.73041.9621-1.0546.1573-0.0783-0.17170.12830.2066-0.07310.0142-0.4118-0.42120.15130.04080.0148-0.01660.0521-0.0070.037247.60772.19455.229
61.84930.01292.48150.04820.34166.3120.03150.0850.0987-0.0076-0.02140.0134-0.08440.1798-0.01020.16430.00620.02580.0922-0.03070.128447.11162.6932.46
72.1521.4721-0.37533.0829-0.59732.30110.19370.06860.40450.5973-0.03840.5668-0.3895-0.1893-0.15540.28050.08380.1310.06680.0380.306134.83856.78628.479
80.81750.17280.17996.2086-0.36024.9426-0.00760.0301-0.0381-0.3352-0.1288-0.19180.21920.28650.13640.04810.00140.02040.03230.01180.093651.55465.00744.825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 116
2X-RAY DIFFRACTION2A117 - 161
3X-RAY DIFFRACTION3A162 - 201
4X-RAY DIFFRACTION4A202 - 244
5X-RAY DIFFRACTION5B1 - 104
6X-RAY DIFFRACTION6B105 - 121
7X-RAY DIFFRACTION7B122 - 211
8X-RAY DIFFRACTION8B212 - 243

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