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- PDB-1hkv: mycobacterium diaminopimelate dicarboxylase (lysa) -

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Basic information

Entry
Database: PDB / ID: 1hkv
Titlemycobacterium diaminopimelate dicarboxylase (lysa)
ComponentsDIAMINOPIMELATE DECARBOXYLASE
KeywordsLYASE / DECARBOXYLASE / DIAMINOPIMELATE / DAPDC / PLP / LYSINE PATHWAY / MYCBACTERIUM TUBERCULOSIS / LYSINE SYNTHETIC PATHWAY / PYRIDOXAL PHOSPHATE / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TB / TBSGC
Function / homology
Function and homology information


diaminopimelate decarboxylase / diaminopimelate decarboxylase activity / 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
LYSINE / PYRIDOXAL-5'-PHOSPHATE / Diaminopimelate decarboxylase / Diaminopimelate decarboxylase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGokulan, K. / Rupp, B. / Pavelka Jr, M.S. / Jacobs Jr, W.R. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of Mycobacterium Tuberculosis Diaminopimelate Decarboxylase, an Essential Enzyme in Bacterial Lysine Biosynthesis
Authors: Gokulan, K. / Rupp, B. / Pavelka, M. / Jacobs, W. / Sacchettini, J.C.
History
DepositionMar 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Structure summary
Revision 1.2May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4686
Polymers96,6792
Non-polymers7894
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)111.452, 111.452, 238.253
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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 3 - 445 / Label seq-ID: 3 - 445

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

NCS oper: (Code: given
Matrix: (-0.275, -0.716, -0.6416), (-0.7167, -0.2921, 0.6332), (-0.6408, 0.634, -0.4329)
Vector: 230.89999, -72.31, 341.79999)

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Components

#1: Protein DIAMINOPIMELATE DECARBOXYLASE / DAP DECARBOXYLASE / MESO-DIAMINOPIMELATE DECARBOXYLASE / LYSA


Mass: 48339.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH COFACTOR PLP AND PRODUCT LYSINE / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Description: C-TERM 6-HIS TAG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) MET-
References: UniProt: P31848, UniProt: P9WIU7*PLUS, diaminopimelate decarboxylase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONVERTS MESOO-2,6-DIAMINOHEPTANEDIOATE TO L-LYSINE AND CO(2). REQUIRES PYRIDOXAL PHOSPHATE AS A ...CONVERTS MESOO-2,6-DIAMINOHEPTANEDIOATE TO L-LYSINE AND CO(2). REQUIRES PYRIDOXAL PHOSPHATE AS A COFACTOR. MEMBER OF THE LYSINE BIOSYNTHESIS PATHWAY AT THE LAST STEP OF LYSINE SYNTHESIS.
Sequence detailsRV1293, INITIAL METHIONINE FROM EXPRESSION CONSTRUCT

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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: 3.9 Å3/Da / Density % sol: 67 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 4 UL HANGING DROPS (2 UL OF DAPDC 10 MG/ML CONTAINING 5MM OF LYSINE COMBINED WITH 2 UL OF WELL SOLUTION) WERE EQUILIBRATED AGAINST 500 UL OF WELL SOLUTION (24% PEG-MME 5K, 0.1M MES BUFFER ...Details: 4 UL HANGING DROPS (2 UL OF DAPDC 10 MG/ML CONTAINING 5MM OF LYSINE COMBINED WITH 2 UL OF WELL SOLUTION) WERE EQUILIBRATED AGAINST 500 UL OF WELL SOLUTION (24% PEG-MME 5K, 0.1M MES BUFFER PH6.3 AND 60 MM AMMONIUM SULFATE). THESE CRYSTALS WERE SOAKED FOR 3 HRS IN IN MOTHER LIQUOR CONTAINING 0.2 MM PLP. THE CRYSTALS ARE DISTINCTLY YELLOW., pH 6.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mMDAP1reservoir
20.2 mMPLP1reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.97918
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2002 / Details: DOUBLE MONO
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→65.5 Å / Num. obs: 44373 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.6
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 3.1 / % possible all: 94
Reflection
*PLUS
Lowest resolution: 18 Å / Num. measured all: 276375
Reflection shell
*PLUS
% possible obs: 94 % / Num. unique obs: 3160 / Num. measured obs: 19682

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HKW

1hkw


Resolution: 2.6→18 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.57 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM OXT OF A 447 AND B 447 WERE REMOVED IN ORDER TO INDICATE THAT THE CHAINS CONTINUE BEYOND RESIDUE 447.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2374 5.1 %RANDOM
Rwork0.224 ---
obs0.227 44373 99.8 %-
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: 47.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 50 236 6946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0216838
X-RAY DIFFRACTIONr_bond_other_d0.0020.026377
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9639318
X-RAY DIFFRACTIONr_angle_other_deg0.858314706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.955890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027731
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021359
X-RAY DIFFRACTIONr_nbd_refined0.2280.21559
X-RAY DIFFRACTIONr_nbd_other0.2590.27919
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.10.24447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2199
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.3480.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1321.54428
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04227120
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.80532410
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4744.52198
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.38 171
Rwork0.392 3160
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.03
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.657
LS refinement shell
*PLUS
Rfactor Rfree: 0.38

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