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- PDB-4d9i: Crystal structure of holo Diaminopropionate ammonia lyase from Es... -

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Basic information

Entry
Database: PDB / ID: 4d9i
TitleCrystal structure of holo Diaminopropionate ammonia lyase from Escherichia coli
ComponentsDiaminopropionate ammonia-lyase
KeywordsLYASE / Fold type II PLP-dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily
Function / homology
Function and homology information


diaminopropionate ammonia-lyase / diaminopropionate ammonia-lyase activity / pyridoxal phosphate binding / protein homodimerization activity
Similarity search - Function
Diaminopropionate ammonia-lyase / Diaminopropionate ammonia-lyase, subgroup / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Diaminopropionate ammonia-lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBisht, S. / Rajaram, V. / Bharath, S.R. / Murthy, M.R.N.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis
Authors: Bisht, S. / Rajaram, V. / Bharath, S.R. / Kalyani, J.N. / Khan, F. / Rao, A.N. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2May 10, 2017Group: Structure summary
Revision 1.3Nov 8, 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
Revision 1.4Dec 6, 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

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Assembly

Deposited unit
A: Diaminopropionate ammonia-lyase
B: Diaminopropionate ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4454
Polymers87,2012
Non-polymers2442
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint5 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.530, 85.530, 207.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Diaminopropionate ammonia-lyase / Diaminopropionatase / Alpha / beta-diaminopropionate ammonia-lyase


Mass: 43600.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2871, JW2839, ygeX / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P66899, diaminopropionate ammonia-lyase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 20% PEG 3350, 70mM magnesium chloride, 50mM lithium sulfate, 6mM sodium citrate, 40mM tris HCl pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2010 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 52570 / % possible obs: 99.2 % / Redundancy: 5 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2454 / % possible all: 93.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D9G

4d9g


Resolution: 2→19.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.984 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23254 2662 5.1 %RANDOM
Rwork0.19223 ---
obs0.19433 49610 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.458 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 16 426 6332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.026033
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9548202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5645779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24525.04250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19515947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2161520
X-RAY DIFFRACTIONr_chiral_restr0.080.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214546
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 173 -
Rwork0.262 3147 -
obs--93.68 %
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)
14.46090.11870.89510.68240.11052.2130.067-0.8632-0.23470.0444-0.11660.1720.1868-0.27180.04950.061-0.02650.0070.4182-0.02490.1526.5348.09281.831
24.06060.27240.89312.57180.17753.3131-0.00940.29890.1845-0.3009-0.07440.393-0.0442-0.33210.08390.13360.0355-0.08460.3143-0.03050.236320.52655.98561.086
34.91260.48320.15791.10650.34292.44880.0274-0.910.28790.1039-0.17880.2011-0.1151-0.27580.15150.0253-0.0260.01130.5432-0.13360.193220.87653.63383.879
45.34810.3835-0.28390.91970.09592.1060.0443-1.15220.49210.1278-0.12950.0695-0.149-0.07590.08510.035-0.0038-0.0190.5301-0.16620.145536.5956.98287.132
53.0991-0.47871.72921.7091-0.91242.10290.15960.49460.0491-0.0753-0.2726-0.26870.17490.45930.11290.07950.040.01650.33280.00720.101670.78550.11773.649
66.0346-1.22432.7141.8729-0.5014.2844-0.0767-0.86020.15270.33890.0665-0.2517-0.0231-0.2930.01010.1013-0.0303-0.05330.3379-0.00290.123775.85147.31596.104
73.3763-0.54421.92741.3653-1.00323.4077-0.04630.33950.40280.0263-0.2273-0.3228-0.11660.4740.27350.01350.0120.0120.29810.06480.196278.04353.22579.916
84.3538-0.18180.62351.3153-1.04212.6035-0.0943-0.16770.66090.0117-0.1639-0.1912-0.25960.11830.25810.03640.0014-0.02720.2191-0.02210.173963.59159.43376.906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 90
2X-RAY DIFFRACTION2A91 - 186
3X-RAY DIFFRACTION3A187 - 298
4X-RAY DIFFRACTION4A299 - 397
5X-RAY DIFFRACTION5B2 - 64
6X-RAY DIFFRACTION6B65 - 176
7X-RAY DIFFRACTION7B177 - 274
8X-RAY DIFFRACTION8B275 - 397

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