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- PDB-2qgh: Crystal structure of diaminopimelate decarboxylase from Helicobac... -

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Basic information

Entry
Database: PDB / ID: 2qgh
TitleCrystal structure of diaminopimelate decarboxylase from Helicobacter pylori complexed with L-lysine
ComponentsDiaminopimelate decarboxylase
KeywordsLYASE / Diaminopimelate Decarboxylase
Function / homology
Function and homology information


diaminopimelate decarboxylase / diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate / pyridoxal phosphate binding
Similarity search - Function
Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / 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 ...Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / 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
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHu, T. / Wu, D. / Jiang, H. / Shen, X.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of diaminopimelate decarboxylase from Helicobacter pylori complexed with L-lysine
Authors: Hu, T. / Wu, D. / Jiang, H. / Shen, X.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 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_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_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: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9604
Polymers47,4741
Non-polymers4863
Water2,180121
1
A: Diaminopimelate decarboxylase
hetero molecules

A: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9208
Polymers94,9472
Non-polymers9736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area8780 Å2
ΔGint-34 kcal/mol
Surface area29190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.248, 79.248, 134.275
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Diaminopimelate decarboxylase /


Mass: 47473.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: SS1 / Gene: lysA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: B4XMC6*PLUS, diaminopimelate decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Bicine, 1.6M Ammonium Sulfate, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→19.81 Å / Num. obs: 21635 / % possible obs: 97 % / Redundancy: 7.14 % / Rmerge(I) obs: 0.128 / Χ2: 1.73 / Net I/σ(I): 5.1 / Scaling rejects: 5909
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.18 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / Num. measured all: 15686 / Num. unique all: 2184 / Χ2: 1.41 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
d*TREK7.1SSIdata processing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TWI

1twi


Resolution: 2.3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2136 9.6 %RANDOM
Rwork0.206 ---
obs-21499 96.8 %-
Solvent computationBsol: 41.775 Å2
Displacement parametersBiso mean: 27.231 Å2
Baniso -1Baniso -2Baniso -3
1-1.719 Å20 Å20 Å2
2--1.719 Å20 Å2
3----3.437 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 31 121 3254
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2421.5
X-RAY DIFFRACTIONc_scbond_it1.9752
X-RAY DIFFRACTIONc_mcangle_it2.0032
X-RAY DIFFRACTIONc_scangle_it2.7952.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3NEW_PLP_GOL.PARAM

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