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- PDB-2o0t: The three dimensional structure of diaminopimelate decarboxylase ... -

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Basic information

Entry
Database: PDB / ID: 2o0t
TitleThe three dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation
ComponentsDiaminopimelate decarboxylase
KeywordsLYASE / PLP binding enzyme / Decarboxylase / lysine biosynthesis / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


diaminopimelate decarboxylase / diaminopimelate decarboxylase activity / cell wall / lysine biosynthetic process via diaminopimelate / peptidoglycan-based cell wall / pyridoxal phosphate binding
Similarity search - Function
Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain ...Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Diaminopimelate decarboxylase / Diaminopimelate decarboxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsWeyand, S. / Kefala, G. / Weiss, M.S. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: J Struct Funct Genomics / Year: 2009
Title: The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation.
Authors: Weyand, S. / Kefala, G. / Svergun, D.I. / Weiss, M.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of LysA (Rv1293) from Mycobacterium tuberculosis
Authors: Kefala, G. / Perry, L.J. / Weiss, M.S.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). IT IS AT PRESENT UNCLEAR WHETHER THE BIOLOGICAL UNIT IS A HOMODIMER CONSISTING OF CHAINS A, B AND C, D OR A HOMOTETRAMER CONSISTING OF CHAINS A,B,C,D. SEE REMARK 350 FOR INFORMATION ON GENERATING A TETRAMER

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diaminopimelate decarboxylase
B: Diaminopimelate decarboxylase
C: Diaminopimelate decarboxylase
D: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,8056
Polymers199,6134
Non-polymers1922
Water7,080393
1
A: Diaminopimelate decarboxylase
B: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9994
Polymers99,8072
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-64 kcal/mol
Surface area30410 Å2
MethodPISA
2
C: Diaminopimelate decarboxylase
D: Diaminopimelate decarboxylase


Theoretical massNumber of molelcules
Total (without water)99,8072
Polymers99,8072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-25 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.780, 106.880, 121.930
Angle α, β, γ (deg.)90.00, 104.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 2 / Auth seq-ID: 2 - 446 / Label seq-ID: 4 - 448

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe asymmetric unit of the protein contains a tetramer in the asymmetric unit. It is at present unclear whether the biological unit is a homodimer consisting of chains A and B, or C and D, respectively, or a homotetramer consisting of chains A, B, C and D.

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Components

#1: Protein
Diaminopimelate decarboxylase / / DAP decarboxylase


Mass: 49903.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: lysA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3)pRARE
References: UniProt: P0A5M4, UniProt: P9WIU7*PLUS, diaminopimelate decarboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 291 K
Details: 20-23%(w/v) polyethylene glycol monomethylether 5000, 0.1 M MES, 60 mM ammonium sulfate, pH 6.1-6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 25, 2004
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.33→99 Å / Num. obs: 80203 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.8
Reflection shellResolution: 2.33→2.37 Å / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HKV

1hkv


Resolution: 2.33→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 15.766 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1597 2 %RANDOM
Rwork0.191 ---
obs0.192 78557 99.9 %-
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: 46.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å2-1.52 Å2
2---1.69 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.33→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13350 0 10 393 13753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02213612
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.96418572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48151780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42123.121564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.379152092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.85115116
X-RAY DIFFRACTIONr_chiral_restr0.1230.22196
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210332
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.26433
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.29217
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2717
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9241.59085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6432.514224
X-RAY DIFFRACTIONr_scbond_it4.16655060
X-RAY DIFFRACTIONr_scangle_it5.851104348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1780tight positional0.060.05
2B1780tight positional0.080.05
3C1780tight positional0.070.05
4D1780tight positional0.060.05
1A1539medium positional0.40.5
2B1539medium positional0.470.5
3C1539medium positional0.420.5
4D1539medium positional0.410.5
1A1780tight thermal0.681.5
2B1780tight thermal0.761.5
3C1780tight thermal0.681.5
4D1780tight thermal0.661.5
1A1539medium thermal1.742.5
2B1539medium thermal1.82.5
3C1539medium thermal1.712.5
4D1539medium thermal1.672.5
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 127 -
Rwork0.252 5749 -
obs--99.9 %
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)
11.5321-0.4520.01121.0204-0.01950.829-0.00420.0480.2808-0.1867-0.0290.019-0.0768-0.08070.0332-0.142-0.02060.0068-0.1059-0.0441-0.0001-0.978911.567540.0908
21.4386-0.4851-0.03670.9350.04530.63020.0159-0.2412-0.01560.02-0.003-0.00530.0985-0.0089-0.0129-0.1719-0.02920.0133-0.045-0.028-0.146311.567-12.067155.6523
30.6961-0.12510.14921.512-0.55251.10070.0871-0.0925-0.0128-0.06310.05770.25930.0767-0.1791-0.1448-0.0403-0.0671-0.0162-0.05360.0247-0.0817-22.3321-21.557916.0887
41.1356-0.35020.36611.1701-0.31420.93160.1088-0.0164-0.0505-0.1240.0094-0.06620.12970.0728-0.11810.02420.0027-0.0094-0.1108-0.0455-0.1495.546-35.028216.0628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4474 - 449
2X-RAY DIFFRACTION2BB2 - 4474 - 449
3X-RAY DIFFRACTION3CC2 - 4474 - 449
4X-RAY DIFFRACTION4DD2 - 4474 - 449

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