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- PDB-5ygr: Crystal structure of PLP bound Diaminopropionate ammonia lyase fr... -

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Basic information

Entry
Database: PDB / ID: 5ygr
TitleCrystal structure of PLP bound Diaminopropionate ammonia lyase from Salmonella typhimurium
Components(Diaminopropionate ammonia ...) x 2
KeywordsLYASE / dimer / internal aldimine
Function / homology
Function and homology information


diaminopropionate ammonia-lyase / diaminopropionate ammonia-lyase activity / pyridoxal phosphate binding
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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Diaminopropionate ammonia-lyase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGeeta, D. / Shveta, B. / Shavithri, H.S. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyBT/ PR7021/BRB/10/1142/2012 India
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Comparative structural and enzymatic studies on Salmonella typhimurium diaminopropionate ammonia lyase reveal its unique features
Authors: Deka, G. / Bisht, S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionSep 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diaminopropionate ammonia lyase
B: Diaminopropionate ammonia lyase
C: Diaminopropionate ammonia lyase
D: Diaminopropionate ammonia lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,58824
Polymers180,9194
Non-polymers1,67020
Water10,503583
1
A: Diaminopropionate ammonia lyase
B: Diaminopropionate ammonia lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,99415
Polymers89,9242
Non-polymers1,07113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Diaminopropionate ammonia lyase
D: Diaminopropionate ammonia lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5949
Polymers90,9952
Non-polymers5997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.890, 128.440, 138.100
Angle α, β, γ (deg.)90.00, 110.28, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA8 - 4018 - 401
21GLYGLYBB8 - 4018 - 401
12ASNASNAA8 - 4008 - 400
22ASNASNCC8 - 4008 - 400
13GLYGLYAA8 - 4018 - 401
23GLYGLYDD8 - 4018 - 401
14ALAALABB8 - 4048 - 404
24ALAALACC8 - 4048 - 404
15ALAALABB8 - 4048 - 404
25ALAALADD8 - 4048 - 404
16ALAALACC8 - 4048 - 404
26ALAALADD8 - 4048 - 404

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Diaminopropionate ammonia ... , 2 types, 4 molecules ABCD

#1: Protein Diaminopropionate ammonia lyase


Mass: 44426.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / Gene: ygeX / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: P40817*PLUS, diaminopropionate ammonia-lyase
#2: Protein Diaminopropionate ammonia lyase


Mass: 45497.441 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / Gene: ygeX / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: P40817*PLUS, diaminopropionate ammonia-lyase

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Non-polymers , 4 types, 603 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.43 Å3/Da / Density % sol: 49.45 % / Description: Thin plate like crystals
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.6
Details: 20%(w/v) PEG4000, 20%(v/v) 2-propanol, 100mM sodium citrate pH 5.6, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.956 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2014
RadiationMonochromator: Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 2.5→77.16 Å / Num. obs: 58141 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.07 / Rsym value: 0.15 / Net I/σ(I): 7.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8417 / CC1/2: 0.83 / Rpim(I) all: 0.33 / Rsym value: 0.73 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
iMOSFLMdata processing
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D9G

4d9g


Resolution: 2.5→77 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.871 / SU B: 13.51 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.705 / ESU R Free: 0.35 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29919 2802 4.8 %RANDOM
Rwork0.23651 ---
obs0.23953 55329 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.533 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.5→77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10976 0 98 583 11657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911328
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210168
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.95315430
X-RAY DIFFRACTIONr_angle_other_deg1.107323235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64951496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91724.424434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39151558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3981540
X-RAY DIFFRACTIONr_chiral_restr0.0820.21735
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113130
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022554
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_it3.5564.546029
X-RAY DIFFRACTIONr_mcbond_other3.5534.546028
X-RAY DIFFRACTIONr_mcangle_it5.3316.8017504
X-RAY DIFFRACTIONr_mcangle_other5.3316.8017505
X-RAY DIFFRACTIONr_scbond_it3.5754.6475299
X-RAY DIFFRACTIONr_scbond_other3.5454.6355263
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3556.8787871
X-RAY DIFFRACTIONr_long_range_B_refined8.03536.97213272
X-RAY DIFFRACTIONr_long_range_B_other8.03536.97413273
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A172620.07
12B172620.07
21A197920.05
22C197920.05
31A192530.07
32D192530.07
41B181940.07
42C181940.07
51B191180.06
52D191180.06
61C204150.07
62D204150.07
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 206 -
Rwork0.321 4065 -
obs--99.7 %

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