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- PDB-5d8n: Tomato leucine aminopeptidase mutant - K354E -

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Basic information

Entry
Database: PDB / ID: 5d8n
TitleTomato leucine aminopeptidase mutant - K354E
ComponentsLeucine aminopeptidase 1, chloroplastic
KeywordsHYDROLASE
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
ACETATE ION / Leucine aminopeptidase 1, chloroplastic
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsDuPrez, K.T. / Scranton, M.A. / Walling, L.L. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS 0725093 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural insights into chaperone-activity enhancement by a K354E mutation in tomato acidic leucine aminopeptidase.
Authors: DuPrez, K.T. / Scranton, M.A. / Walling, L.L. / Fan, L.
History
DepositionAug 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Leucine aminopeptidase 1, chloroplastic
B: Leucine aminopeptidase 1, chloroplastic
C: Leucine aminopeptidase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,38527
Polymers167,3793
Non-polymers1,00624
Water23,0591280
1
A: Leucine aminopeptidase 1, chloroplastic
B: Leucine aminopeptidase 1, chloroplastic
C: Leucine aminopeptidase 1, chloroplastic
hetero molecules

A: Leucine aminopeptidase 1, chloroplastic
B: Leucine aminopeptidase 1, chloroplastic
C: Leucine aminopeptidase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,77054
Polymers334,7576
Non-polymers2,01348
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area28790 Å2
ΔGint-336 kcal/mol
Surface area108950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.112, 165.193, 168.275
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 55 - 571 / Label seq-ID: 13 - 529

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 55792.840 Da / Num. of mol.: 3 / Fragment: residues 52-571 / Mutation: K354E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: LAPA1, LAP, LAP2 / Plasmid: pQE11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: Q10712, leucyl aminopeptidase, prolyl aminopeptidase

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Non-polymers , 5 types, 1304 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1280 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, pH 6.5, 0.35 M magnesium acetate, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.15→33.92 Å / Num. obs: 96081 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 15.66 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.043 / Net I/σ(I): 15 / Num. measured all: 702109
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
2.15-2.217.10.65635022470610.264100
9.62-33.926.80.02644.6796511660.01198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
xia20.3.6.3data reduction
xia20.3.6.3data scaling
PHASER2.5.6phasing
Coot0.8.1model building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KSI

4ksi


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1624 / WRfactor Rwork: 0.141 / FOM work R set: 0.8799 / SU B: 7.66 / SU ML: 0.103 / SU R Cruickshank DPI: 0.182 / SU Rfree: 0.1433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1789 2000 2.1 %RANDOM
Rwork0.153 ---
obs0.1535 94010 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.71 Å2 / Biso mean: 30.968 Å2 / Biso min: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---0.35 Å20 Å2
3----0.88 Å2
Refinement stepCycle: final / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11079 0 51 1280 12410
Biso mean--50.07 37.6 -
Num. residues----1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911765
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211264
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.96816016
X-RAY DIFFRACTIONr_angle_other_deg0.956326007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26651616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55825.548456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.223151969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3351555
X-RAY DIFFRACTIONr_chiral_restr0.0810.21858
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0213835
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022454
X-RAY DIFFRACTIONr_mcbond_it2.7481.4046328
X-RAY DIFFRACTIONr_mcbond_other2.7411.4046325
X-RAY DIFFRACTIONr_mcangle_it4.3215.5057988
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A595680.1
12B595680.1
21A593780.1
22C593780.1
31B594060.09
32C594060.09
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 146 -
Rwork0.203 6876 -
all-7022 -
obs--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)
10.26240.3242-0.07250.4436-0.20730.4328-0.11380.13360.056-0.16710.1550.0620.11540.0513-0.04120.0756-0.0426-0.01980.110.00050.04216.1889-48.5207-5.7236
20.49260.38570.2190.32090.13520.2092-0.04560.05610.0226-0.04880.05820.02050.02760.0399-0.01250.0753-0.0080.02330.0783-0.00620.058316.8348-38.98441.2994
30.1064-0.1177-0.030.16450.19030.76180.01560.00340.0312-0.0097-0.003-0.04350.02490.01-0.01250.0509-0.02550.03760.0775-0.00120.076827.0951-20.855920.8027
40.2935-0.0854-0.04250.12780.19270.33260.0206-0.00020.0281-0.0397-0.0148-0.0049-0.0466-0.014-0.00580.0761-0.00880.02730.06060.00560.078612.0737-18.16817.0027
50.2421-0.0869-0.25120.3040.09360.2742-0.01270.0062-0.0117-0.05720.0062-0.01420.0217-0.03120.00650.0766-0.0169-0.01540.0593-0.02320.0722-10.4217-65.347211.1981
60.036-0.04-0.07180.21610.18060.3377-0.00710.0032-0.0067-0.01180.00870.0139-0.0081-0.0904-0.00160.0418-0.02220.00020.0840.00170.0964-26.3839-57.332640.4176
70.35-0.0135-0.06870.04470.14210.4745-0.0161-0.0074-0.00980.01340.0190.00990.04570.0417-0.0030.0744-0.01-0.00440.05840.00790.0827-11.3874-61.536641.6276
80.32120.15150.19410.54-0.31450.5243-0.0142-0.02650.1924-0.0264-0.01950.2061-0.01430.0340.03370.06570.02530.00550.0396-0.00350.1551-15.408710.963531.8603
90.9095-0.02991.21890.0153-0.04951.6422-0.1130.15810.11380.0368-0.0392-0.0053-0.14820.23370.15220.1003-0.04370.01130.08510.06860.08315.512922.179831.4366
101.24880.24770.44760.26030.20950.3722-0.01740.10960.06170.0047-0.0170.03090.01410.09320.03440.09280.01680.02420.06050.02020.0651-7.216912.248725.2411
110.51460.34850.06750.4442-0.11760.1376-0.0288-0.03970.05880.02780.02780.0574-0.0457-0.04730.0010.10340.04380.03040.04820.01310.0704-21.84151.509328.2796
120.1111-0.0418-0.01910.5162-0.15480.08340.01030.0193-0.00930.02590.03630.0262-0.0308-0.0281-0.04660.06250.01580.00480.07840.03010.0732-26.0405-19.412220.401
130.543-0.24720.08740.3780.04880.05810.01860.0176-0.0638-0.03730.0384-0.0273-0.03090.0181-0.0570.08660.00090.02940.07790.01070.0627-10.0715-14.352314.7577
140.2967-0.016-0.07470.5846-0.0570.04080.00910.0411-0.0114-0.05870.0109-0.0321-0.0148-0.0314-0.020.08050.00910.00510.07760.01010.0623-11.2113-19.674517.455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 145
2X-RAY DIFFRACTION2A146 - 284
3X-RAY DIFFRACTION3A285 - 444
4X-RAY DIFFRACTION4A445 - 571
5X-RAY DIFFRACTION5B55 - 284
6X-RAY DIFFRACTION6B285 - 444
7X-RAY DIFFRACTION7B445 - 571
8X-RAY DIFFRACTION8C55 - 98
9X-RAY DIFFRACTION9C99 - 145
10X-RAY DIFFRACTION10C146 - 212
11X-RAY DIFFRACTION11C213 - 284
12X-RAY DIFFRACTION12C285 - 444
13X-RAY DIFFRACTION13C445 - 488
14X-RAY DIFFRACTION14C489 - 571

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