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- PDB-3n2b: 1.8 Angstrom Resolution Crystal Structure of Diaminopimelate Deca... -

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Basic information

Entry
Database: PDB / ID: 3n2b
Title1.8 Angstrom Resolution Crystal Structure of Diaminopimelate Decarboxylase (lysA) from Vibrio cholerae.
ComponentsDiaminopimelate decarboxylase
KeywordsLYASE / Diaminopimelate Decarboxylase / lysA / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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, 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
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.8 Angstrom Resolution Crystal Structure of Diaminopimelate Decarboxylase (lysA) from Vibrio cholerae.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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_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_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

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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)196,4488
Polymers196,3064
Non-polymers1424
Water20,1951121
1
A: Diaminopimelate decarboxylase
B: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1883
Polymers98,1532
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-28 kcal/mol
Surface area30600 Å2
MethodPISA
2
C: Diaminopimelate decarboxylase
D: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2595
Polymers98,1532
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-27 kcal/mol
Surface area31150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.394, 80.329, 118.693
Angle α, β, γ (deg.)105.31, 93.62, 90.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Diaminopimelate decarboxylase / / DAP decarboxylase


Mass: 49076.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: lysA, VC_0125 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9KVL7, diaminopimelate decarboxylase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1121 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein solution: 7.8 mg/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3; Screen solution: PACT (D8) 0.2M Ammonium chloride, 0.1M Tris pH 8.0, 20%(w/v) PEG6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 147832 / Num. obs: 147832 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7354 / % possible all: 96.2

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P3E

2p3e


Resolution: 1.8→29.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.264 / SU ML: 0.07 / Isotropic thermal model: Refined individually / Cross valid method: THROUGHOUT / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21874 7289 5 %RANDOM
Rwork0.18266 ---
all0.18449 138491 --
obs0.18449 138491 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.855 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20.34 Å2-0.25 Å2
2---2.98 Å2-1.49 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12599 0 4 1121 13724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213140
X-RAY DIFFRACTIONr_bond_other_d0.0010.028871
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.96717859
X-RAY DIFFRACTIONr_angle_other_deg0.846321603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.24351661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.45123.894624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.495152214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.37315103
X-RAY DIFFRACTIONr_chiral_restr0.0890.21997
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022679
X-RAY DIFFRACTIONr_mcbond_it1.2141.58187
X-RAY DIFFRACTIONr_mcbond_other0.3271.53336
X-RAY DIFFRACTIONr_mcangle_it2.072213169
X-RAY DIFFRACTIONr_scbond_it2.92834953
X-RAY DIFFRACTIONr_scangle_it4.634.54688
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 539 -
Rwork0.266 10039 -
obs-10039 96.33 %

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