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- PDB-1yl5: Crystal structure of Mycobacterium tuberculosis dihydrodipicolina... -

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Basic information

Entry
Database: PDB / ID: 1yl5
TitleCrystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (RV2773C) (crystal form A)
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: 2.3 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_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_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)51,8604
Polymers51,8112
Non-polymers492
Water88349
1
A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules

A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7198
Polymers103,6224
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area12150 Å2
ΔGint-104 kcal/mol
Surface area38560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.26, 122.00, 77.93
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
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: 25905.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dapB / Plasmid: PETM-11 / 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.: 49 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris/HCl, 20 % PEG 3350, 120 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: 1.1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2004
RadiationMonochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. all: 25757 / Num. obs: 25757 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 63.1 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.1
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.75 / Num. unique all: 1256 / % possible all: 99.1

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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

1p9l


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 16.266 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.294 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24924 1056 4.1 %RANDOM
Rwork0.20514 ---
all0.20697 24648 --
obs0.20697 24648 99.65 %-
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: 54.607 Å2
Baniso -1Baniso -2Baniso -3
1-3.79 Å20 Å20 Å2
2---3.04 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 2 49 3699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223718
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9675072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9415492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48323.562146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75815572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7791526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022810
X-RAY DIFFRACTIONr_nbd_refined0.2240.21789
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.210
X-RAY DIFFRACTIONr_mcbond_it0.8541.52503
X-RAY DIFFRACTIONr_mcangle_it1.5472.53938
X-RAY DIFFRACTIONr_scbond_it3.92451304
X-RAY DIFFRACTIONr_scangle_it6.212101134
LS refinement shellResolution: 2.3→2.424 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.348 146 -
Rwork0.278 3489 -
obs-3489 99.26 %
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)
15.08931.28211.42733.88770.53758.11780.12180.0260.12850.5408-0.25670.3221-0.1507-0.31430.1349-0.1342-0.1240.0578-0.1005-0.0198-0.17511.659239.9977-3.769
21.30130.4440.20933.3239-0.12240.0455-0.03870.00280.0732-0.36030.00240.43050.172-0.30620.0363-0.0487-0.0221-0.059-0.053-0.0045-0.019715.972457.134319.1921
31.5829-0.4116-0.30673.89750.41564.5313-0.102-0.1889-0.0110.0150.032-0.1305-0.09680.15460.07-0.2634-0.0408-0.0190.01340.0088-0.054725.65833.839444.883
42.44741.20970.08381.8315-0.20261.64340.0265-0.1047-0.4711-0.151-0.1123-0.39520.30810.09660.0858-0.02360.02280.0065-0.14820.01520.007735.966548.453521.9664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1051 - 107
2X-RAY DIFFRACTION1AA218 - 245220 - 247
3X-RAY DIFFRACTION2AA106 - 217108 - 219
4X-RAY DIFFRACTION3BB0 - 1051 - 107
5X-RAY DIFFRACTION3BB218 - 245220 - 247
6X-RAY DIFFRACTION4BB106 - 217108 - 219

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