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- PDB-3kr4: Structure of a protease 3 -

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Basic information

Entry
Database: PDB / ID: 3kr4
TitleStructure of a protease 3
ComponentsM17 leucyl aminopeptidase
KeywordsHYDROLASE / protease / Aminopeptidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / identical protein binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 ...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
Chem-BES / CARBONATE ION / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcGowan, S. / Whisstock, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases
Authors: McGowan, S. / Oellig, C.A. / Birru, W.A. / Caradoc-Davies, T.T. / Stack, C.M. / Lowther, J. / Skinner-Adams, T. / Mucha, A. / Kafarski, P. / Grembecka, J. / Trenholme, K.R. / Buckle, A.M. / ...Authors: McGowan, S. / Oellig, C.A. / Birru, W.A. / Caradoc-Davies, T.T. / Stack, C.M. / Lowther, J. / Skinner-Adams, T. / Mucha, A. / Kafarski, P. / Grembecka, J. / Trenholme, K.R. / Buckle, A.M. / Gardiner, D.L. / Dalton, J.P. / Whisstock, J.C.
History
DepositionNov 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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_atom_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
G: M17 leucyl aminopeptidase
H: M17 leucyl aminopeptidase
I: M17 leucyl aminopeptidase
J: M17 leucyl aminopeptidase
K: M17 leucyl aminopeptidase
L: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)720,166111
Polymers704,50812
Non-polymers15,65899
Water87,5174858
1
A: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,82255
Polymers352,2546
Non-polymers7,56849
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27840 Å2
ΔGint-132 kcal/mol
Surface area96940 Å2
MethodPISA
2
G: M17 leucyl aminopeptidase
H: M17 leucyl aminopeptidase
I: M17 leucyl aminopeptidase
J: M17 leucyl aminopeptidase
K: M17 leucyl aminopeptidase
L: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,34456
Polymers352,2546
Non-polymers8,09150
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27870 Å2
ΔGint-127 kcal/mol
Surface area98410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.561, 178.121, 230.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21G
12B
22H
13C
23I
14D
24J
15E
25K

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 1

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA86 - 6033 - 520
21ASPASPGG86 - 6033 - 520
12ASPASPBB86 - 6033 - 520
22ASPASPHH86 - 6033 - 520
13ASPASPCC86 - 6033 - 520
23ASPASPII86 - 6033 - 520
14ASPASPDD86 - 6033 - 520
24ASPASPJJ86 - 6033 - 520
15ASNASNEE86 - 6023 - 519
25ASPASPKK86 - 6033 - 520

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
M17 leucyl aminopeptidase / Malarial protease


Mass: 58708.973 Da / Num. of mol.: 12 / Fragment: residues 84-605 / Mutation: N152Q, N515Q, N546Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: pTrc-His2b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Rosetta2 / References: UniProt: Q8IL11, leucyl aminopeptidase

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Non-polymers , 7 types, 4957 molecules

#2: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN


Mass: 308.373 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H24N2O4 / Comment: protease inhibitor*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#7: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4858 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSo4, 1mM TCEP, 1mM MgCl2, 1mM Bestatin, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95659 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2009
RadiationMonochromator: double crystal silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95659 Å / Relative weight: 1
ReflectionResolution: 2→62.14 Å / Num. obs: 469417 / % possible obs: 98.5 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.251 / Rsym value: 0.069 / Net I/σ(I): 11.3 / Num. measured all: 6476290
Reflection shellResolution: 2→2.11 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.999 / Mean I/σ(I) obs: 2.5 / Num. unique all: 786785 / Rsym value: 0.291 / % possible all: 96.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0063refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KQX

3kqx


Resolution: 2→43.15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.144 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24193 23578 5 %RANDOM
Rwork0.1921 ---
obs0.19459 445463 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.56 Å2 / Biso mean: 12.427 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.68 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 2→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47378 0 780 4858 53016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02248996
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.97366267
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42556155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86225.3131980
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.927158190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.38115104
X-RAY DIFFRACTIONr_chiral_restr0.1220.27586
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02136124
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_it0.8021.530620
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.469249221
X-RAY DIFFRACTIONr_scbond_it2.603318376
X-RAY DIFFRACTIONr_scangle_it4.2224.517040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3949TIGHT POSITIONAL0.070.05
1A3949TIGHT THERMAL0.170.5
2B3862TIGHT POSITIONAL0.060.05
2B3862TIGHT THERMAL0.150.5
3C3934TIGHT POSITIONAL0.050.05
3C3934TIGHT THERMAL0.160.5
4D3908TIGHT POSITIONAL0.080.05
4D3908TIGHT THERMAL0.170.5
5E3874TIGHT POSITIONAL0.090.05
5E3874TIGHT THERMAL0.160.5
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 1679 -
Rwork0.297 31489 -
obs--94.82 %
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)
10.535-0.0184-0.18940.20540.00260.2273-0.0062-0.05850.00880.02530.01590.0148-0.023-0.0426-0.00980.04340.0167-0.0110.04540.00020.024873.63182.81740.179
20.32920.00990.1430.16060.07930.4024-0.002-0.00560.020.00970.0315-0.09540.01510.0841-0.02940.0283-0.00170.00920.0396-0.00690.0945119.66869.46913.438
30.2832-0.1344-0.15220.37320.22090.3532-0.00920.0563-0.0622-0.0476-0.03240.02220.0101-0.05070.04170.0338-0.0024-0.00280.0530.01040.039171.35558.107-8.823
40.3265-0.1371-0.05690.32570.0370.189-0.0239-0.0308-0.00850.02610.01350.06090.0051-0.06170.01030.0284-0.01990.00580.06770.01320.032256.97241.80927.268
50.16120.03960.08130.20060.06890.4581-0.01870.0334-0.0282-0.03610.0169-0.0260.01640.02360.00190.03040.00920.0090.03590.00610.059105.70730.9576.023
60.6330.0573-0.0050.41390.02040.26130.011-0.08940.03080.06890.0019-0.10210.00750.0262-0.0130.05820.0167-0.02420.07420.00750.0356101.08655.00253.894
70.5225-0.0333-0.12890.17630.03580.172-0.0049-0.0723-0.00080.02580.01360.0198-0.0106-0.0332-0.00860.04540.0155-0.01160.0441-0.00040.028576.30982.81155.343
80.3635-0.00510.15450.21280.09920.4413-0.0052-0.00510.02150.01210.0252-0.10920.01830.0893-0.020.0286-0.00130.01320.0434-0.00650.0799122.40969.436128.769
90.2641-0.086-0.12170.36430.19970.3331-0.01910.0565-0.0594-0.0567-0.01460.020.0104-0.03720.03370.034-0.0022-0.00360.05240.00040.033873.59658.097106.452
100.3672-0.1413-0.11060.38750.04610.1935-0.0153-0.0179-0.00060.02420.00750.0606-0.0007-0.06730.00790.0312-0.02-0.00460.06570.00690.034959.5441.814142.3
110.12230.02470.07050.1930.06520.4762-0.01590.033-0.0346-0.04120.0209-0.02080.01350.0168-0.00510.03470.0060.00750.0377-0.00330.0664108.33130.918121.082
120.76010.05690.02190.44320.01910.2105-0.0062-0.07240.0530.06490.0076-0.09380.0040.0368-0.00130.05230.0149-0.02110.07310.00920.0326104.54155.56169.33
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 603
2X-RAY DIFFRACTION2B86 - 603
3X-RAY DIFFRACTION3C86 - 603
4X-RAY DIFFRACTION4D86 - 603
5X-RAY DIFFRACTION5E86 - 602
6X-RAY DIFFRACTION6F86 - 603
7X-RAY DIFFRACTION7G86 - 603
8X-RAY DIFFRACTION8H86 - 603
9X-RAY DIFFRACTION9I86 - 603
10X-RAY DIFFRACTION10J86 - 603
11X-RAY DIFFRACTION11K86 - 603
12X-RAY DIFFRACTION12L86 - 603

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