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- PDB-4d9n: Crystal structure of Diaminopropionate ammonia lyase from Escheri... -

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Basic information

Entry
Database: PDB / ID: 4d9n
TitleCrystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine
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
D-SERINE / Diaminopropionate ammonia-lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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)87,4114
Polymers87,2012
Non-polymers2102
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-5 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.611, 85.611, 207.652
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-DSN / D-SERINE


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
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. Crystals were soaked with 10mM D-ser in crystallization condition for 10 hrs before ...Details: 20% PEG 3350, 70mM magnesium chloride, 50mM lithium sulfate, 6mM sodium citrate, 40mM tris HCl pH 8.3. Crystals were soaked with 10mM D-ser in crystallization condition for 10 hrs before data collection., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 29, 2010 / Details: mirror
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 27635 / % possible obs: 99.8 % / Redundancy: 9.5 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 31.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1311 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D9I

4d9i


Resolution: 2.5→45.57 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.887 / SU B: 22.865 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.977 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26738 1377 5 %RANDOM
Rwork0.21713 ---
obs0.21956 26023 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.121 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5907 0 14 101 6022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.9548209
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4075777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87124.863255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00215947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1391524
X-RAY DIFFRACTIONr_chiral_restr0.0580.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214572
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: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 75 -
Rwork0.288 1668 -
obs--96.94 %
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)
12.0027-0.00980.21840.45450.05810.89610.0467-0.0528-0.1717-0.1032-0.09050.09590.1864-0.11060.04380.1118-0.0259-0.0250.3296-0.04350.210123.69348.71974.336
23.24240.64450.25070.2769-0.36311.7733-0.0415-0.09460.1744-0.0186-0.05860.0916-0.0678-0.20230.10010.08360.0136-0.00880.2904-0.08130.210921.77955.56273.283
35.3909-0.4246-0.79322.52591.67091.93820.0949-0.4290.7055-0.0991-0.12040.3902-0.2756-0.22770.02550.0751-0.00330.03250.4804-0.13820.250720.39360.2887.264
42.25390.0495-0.9230.62180.48161.57810.0288-0.4310.150.0033-0.0727-0.0799-0.12410.03690.0440.094-0.0138-0.03570.4303-0.07550.209137.82157.3487.546
51.6735-0.19281.22610.866-0.35251.30140.14590.0178-0.09090.098-0.078-0.08130.19330.0022-0.06780.15030.0151-0.01540.2996-0.00150.178474.41946.53985.59
61.7563-0.39341.26730.4298-0.60752.2352-0.030.03180.17280.0446-0.1426-0.1611-0.09590.12170.17270.1102-0.017-0.00920.29380.00540.198876.42153.31285.846
70.10031.3842-0.212119.9809-3.11590.87260.2587-0.0558-0.11762.843-0.7389-2.309-0.83920.51690.48020.8345-0.4642-0.34640.65520.04490.692979.25565.03180.738
82.7370.0789-0.18810.4788-0.47231.1575-0.0406-0.1510.2469-0.019-0.09470.0339-0.06860.03340.13520.13390.0054-0.02430.3132-0.02350.198660.36759.00575.666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 143
2X-RAY DIFFRACTION2A144 - 244
3X-RAY DIFFRACTION3A245 - 302
4X-RAY DIFFRACTION4A303 - 397
5X-RAY DIFFRACTION5B2 - 145
6X-RAY DIFFRACTION6B146 - 263
7X-RAY DIFFRACTION7B264 - 302
8X-RAY DIFFRACTION8B303 - 397

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