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- PDB-4ksi: Crystal Structure Analysis of the Acidic Leucine Aminopeptidase o... -

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Basic information

Entry
Database: PDB / ID: 4ksi
TitleCrystal Structure Analysis of the Acidic Leucine Aminopeptidase of Tomato
ComponentsLeucine aminopeptidase 1, chloroplastic
KeywordsHYDROLASE / Exoprotease / defense response / Peptide binding / Divalent metal binding
Function / homology
Function and homology information


prolyl aminopeptidase / leucyl aminopeptidase / protein hexamerization / metalloaminopeptidase activity / chloroplast / peptidase activity / manganese ion binding / magnesium ion binding / proteolysis / cytoplasm
Similarity search - Function
Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases ...Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Leucine aminopeptidase 1, chloroplastic
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDuPrez, K.T. / Scranton, M. / Walling, L. / Fan, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of tomato wound-induced leucine aminopeptidase sheds light on substrate specificity.
Authors: Duprez, K. / Scranton, M.A. / Walling, L.L. / Fan, L.
History
DepositionMay 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Leucine aminopeptidase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,78815
Polymers55,7931
Non-polymers99514
Water8,503472
1
A: Leucine aminopeptidase 1, chloroplastic
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)340,72690
Polymers334,7576
Non-polymers5,96984
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area40590 Å2
ΔGint-638 kcal/mol
Surface area105070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.597, 160.597, 104.183
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Leucine aminopeptidase 1, chloroplastic / DR57 / Leucyl aminopeptidase 1 / LAP 1 / Proline aminopeptidase 1 / Prolyl aminopeptidase 1


Mass: 55792.906 Da / Num. of mol.: 1 / Fragment: Mature LAP-A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: LAP, LAP2, LAPA1 / Plasmid: pQE11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q10712, leucyl aminopeptidase, prolyl aminopeptidase

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Non-polymers , 7 types, 486 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 3.48 Å3/Da / Density % sol: 64.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 0.1 M ammonium sulfate, 45% (v/v) MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 8, 2011 / Details: VariMax HF
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 38529 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.9 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 23.618
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 16.6 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 5.256 / Num. unique all: 2551 / Rsym value: 0.628 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.14 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.747 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(I): 5 / ESU R: 0.145 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1735 2033 5 %RANDOM
Rwork0.13674 ---
obs0.13854 38529 99.9 %-
all-40562 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.377 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 58 472 4312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194182
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9785728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29725.647170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30415724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6651521
X-RAY DIFFRACTIONr_chiral_restr0.1150.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213176
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 120 -
Rwork0.154 2551 -
obs-2551 100 %
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)
11.5532-0.6825-0.14090.5918-0.09930.4115-0.0375-0.0995-0.23750.07650.13660.162-0.0534-0.1071-0.09910.1043-0.0061-0.00360.11150.02370.111232.286-61.92322.187
20.70910.2669-0.32130.5883-0.26930.5005-0.0134-0.0319-0.0009-0.00310.02670.03210.03110.0135-0.01330.0544-0.0025-0.030.0349-0.0090.025839.238-52.62710.693
30.43720.1339-0.0050.27140.04060.2979-0.02150.02090.0438-0.026-0.0040.0352-0.0169-0.0070.02550.04430.0048-0.02220.0315-0.00080.015957.653-33.7416.845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 145
2X-RAY DIFFRACTION2A146 - 284
3X-RAY DIFFRACTION3A285 - 571

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