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- PDB-1yl6: crystal structure of Mycobacterium tuberculosis dihydrodipicolina... -

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Basic information

Entry
Database: PDB / ID: 1yl6
Titlecrystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) (crystal form B)
ComponentsDihydrodipicolinate reductase4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / lysine biosynthesis / dihydrodipicolinate / reductase / NADH / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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 / cell wall / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NADPH binding / peptidoglycan-based cell wall / 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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJanowski, R. / Kefala, G. / Weiss, M.S. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms.
Authors: Janowski, R. / Kefala, G. / Weiss, M.S.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4554
Polymers51,4062
Non-polymers492
Water362
1
A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules

A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9108
Polymers102,8134
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area11950 Å2
ΔGint-91 kcal/mol
Surface area38840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.13, 89.46, 77.52
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: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 40 - 242 / Label seq-ID: 40 - 242

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsTHE SECOND PART OF THE BIOLOGICAL ASSEMBLY (TETRAMER) IS GENERATED BY THE TWO FOLD AXIS: 1/2, 1/2, Z.

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Components

#1: Protein Dihydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase / DHPR


Mass: 25703.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dapB / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP
References: UniProt: P72024, UniProt: P9WP23*PLUS, EC: 1.3.1.26
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.9 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris/HCl, 24 % PEG 3350, 140 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2003
RadiationMonochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→99 Å / Num. all: 13831 / Num. obs: 13831 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 31.1 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.9
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 4 / Num. unique all: 657 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P9L
Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 38.566 / SU ML: 0.33 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.25689 1237 9 %RANDOM
Rwork0.19883 ---
all0.20415 12552 --
obs0.20415 12552 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.521 Å2
Baniso -1Baniso -2Baniso -3
1-5.16 Å20 Å20 Å2
2--1.52 Å20 Å2
3----6.68 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 2 2 3626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223692
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9675038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.64923.562146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.8915566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0871526
X-RAY DIFFRACTIONr_chiral_restr0.0960.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022794
X-RAY DIFFRACTIONr_nbd_refined0.2410.21695
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22563
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.27
X-RAY DIFFRACTIONr_mcbond_it0.7391.52474
X-RAY DIFFRACTIONr_mcangle_it1.3672.53908
X-RAY DIFFRACTIONr_scbond_it3.91551296
X-RAY DIFFRACTIONr_scangle_it6.644101130
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
812tight positional0.050.05
710medium positional0.350.5
812tight thermal0.41.5
710medium thermal1.152.5
LS refinement shellResolution: 2.9→3.055 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.38 182 -
Rwork0.257 1780 -
obs-1780 99.44 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.72060.6284-0.03473.8409-1.30267.0423-0.10380.03710.1740.0511-0.0839-0.1135-0.30890.99970.1877-0.1661-0.1688-0.07280.12640.0306-0.141563.021464.97114.6897
22.90751.43630.18914.12810.10632.95350.0840.2878-0.18340.01680.3328-0.6743-0.17740.7125-0.4168-0.34420.117-0.0201-0.0607-0.132-0.044457.54847.800427.1461
33.5993-0.60961.45625.2191-0.30448.2294-0.1148-0.1044-0.0880.0339-0.1621-0.0412-1.4034-0.27140.2770.06920.06990.0025-0.30590.0336-0.212149.040572.176352.5786
43.81161.45520.26363.3834-0.22973.76430.17980.12480.59770.30780.02560.6469-0.6766-0.3061-0.2054-0.17720.18510.1263-0.26590.09160.005737.999557.884430.0157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1051 - 105
2X-RAY DIFFRACTION1AA218 - 245218 - 245
3X-RAY DIFFRACTION2AA106 - 217106 - 217
4X-RAY DIFFRACTION3BB1 - 1051 - 105
5X-RAY DIFFRACTION3BB218 - 245218 - 245
6X-RAY DIFFRACTION4BB106 - 217106 - 217

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