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- PDB-3l21: The crystal structure of a dimeric mutant of dihydrodipicolinate ... -

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Basic information

Entry
Database: PDB / ID: 3l21
TitleThe crystal structure of a dimeric mutant of dihydrodipicolinate synthase (DAPA, RV2753C) from Mycobacterium Tuberculosis - DHDPS-A204R
ComponentsDihydrodipicolinate synthase
KeywordsTRANSFERASE / dihydrodipicolinate synthase / DHDPS / dapA / dimer / RV2753C / Mycobacterium tuberculosis / lysine biosynthesis / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Lyase / Schiff base
Function / homology
Function and homology information


(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / plasma membrane / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / PYRUVIC ACID / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEvans, G.L. / Schuldt, L. / Jamerson, G.B. / Devenish, S.R. / Weiss, M.S. / Gerrard, J.A.
CitationJournal: To be Published
Title: A dimeric mutant of DHDPS from Mycobacterium tuberculosis
Authors: Evans, G.L. / Schuldt, L. / Griffin, M.D. / Perugini, M.A. / Jamerson, G.B. / Devenish, S.R. / Weiss, M.S. / Gerrard, J.A.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 16, 2018Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.version
Revision 1.3Nov 1, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2
Revision 2.1Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
E: Dihydrodipicolinate synthase
F: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,36064
Polymers188,5076
Non-polymers4,85358
Water28,7521596
1
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,91227
Polymers62,8362
Non-polymers2,07725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-14 kcal/mol
Surface area20760 Å2
MethodPISA
2
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,27519
Polymers62,8362
Non-polymers1,43917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-13 kcal/mol
Surface area20300 Å2
MethodPISA
3
E: Dihydrodipicolinate synthase
F: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,17318
Polymers62,8362
Non-polymers1,33816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-15 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.830, 188.830, 130.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 6 - 300 / Label seq-ID: 10 - 304

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Dihydrodipicolinate synthase / DHDPS


Mass: 31417.824 Da / Num. of mol.: 6 / Mutation: A204R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dapA, MT2823, MTV002.18c, Rv2753c / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pGroESL
References: UniProt: P63945, UniProt: P9WP25*PLUS, dihydrodipicolinate synthase

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Non-polymers , 7 types, 1654 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1596 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.0M ammonium sulfate, 100mM sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2008
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. all: 157209 / Num. obs: 155951 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.052 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.5 / % possible all: 97.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild-type M. tuberculosis DHDPS, PDB ENTRY 1XXX

1xxx


Resolution: 2.1→28.51 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.677 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. TYR117 IS PART OF A HIGHLY CONSERVED LOOP THAT IN OTHER DHDPS STRUCTURES ALSO HAS UNFAVOURABLE RAMACHANDRAN VALUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.20389 4197 3.1 %RANDOM
Rwork0.17849 ---
obs0.17926 130491 98.54 %-
all-151456 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.177 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12875 0 293 1596 14764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.522.00318303
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15251798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00423.361479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.573152005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.35215102
X-RAY DIFFRACTIONr_chiral_restr0.0950.22165
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110058
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.27289
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.29260
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.21418
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.2137
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.04328895
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.607314147
X-RAY DIFFRACTIONr_scbond_it3.1084.54557
X-RAY DIFFRACTIONr_scangle_it4.10864153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2035 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.41
Bmedium positional0.541
Cmedium positional0.441
Dmedium positional0.441
Emedium positional0.321
Fmedium positional0.311
Amedium thermal2.524
Bmedium thermal2.454
Cmedium thermal2.184
Dmedium thermal1.834
Emedium thermal1.814
Fmedium thermal1.964
LS refinement shellResolution: 2.1→2.213 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.234 946 -
Rwork0.196 18469 -
obs--98.96 %
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)
10.42790.05370.1030.57850.07990.4939-0.0352-0.00620.01450.02260.0347-0.02710.010.04230.00050.00460.0035-0.00250.0057-0.0020.002119.4521182.3516103.8678
20.6425-0.0881-0.03710.58560.36441.07630.01560.0153-0.0077-0.0452-0.07250.0316-0.1035-0.15130.0570.01030.0151-0.00580.0223-0.00860.003492.7135199.762992.7486
30.4629-0.2830.00060.81160.08460.57140.03490.0438-0.0118-0.004-0.021-0.09620.05440.0812-0.0140.02250.03620.00350.05950.01040.0744157.4727188.1958112.2049
40.9578-0.3460.04960.5208-0.13810.66260.06030.02940.1459-0.0181-0.0344-0.0874-0.05020.059-0.02590.0222-0.01140.01360.01230.00520.0473139.3176216.026118.8736
50.898-0.19410.0530.4566-0.0360.5943-0.0324-0.1129-0.13160.01640.05380.00430.0954-0.0191-0.02140.06380.05020.0320.06460.04630.0545131.5963161.2011140.7828
60.95720.0286-0.14810.409-0.07280.4743-0.0247-0.17540.12650.0899-0.0059-0.0416-0.12330.01970.03050.1110.0765-0.02760.1141-0.01690.0848154.1434182.9046153.3475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 300
2X-RAY DIFFRACTION2B6 - 300
3X-RAY DIFFRACTION3C6 - 300
4X-RAY DIFFRACTION4D6 - 300
5X-RAY DIFFRACTION5E6 - 300
6X-RAY DIFFRACTION6F6 - 300

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