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- PDB-4fwh: Crystal structure of the Lon-like protease MtaLonC in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4fwh
TitleCrystal structure of the Lon-like protease MtaLonC in complex with MG262
ComponentsTTC1975 peptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Lon protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / ATP binding
Similarity search - Function
Lon protease, AAA domain / LonB-like, AAA domain / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Helicase, Ruva Protein; domain 3 - #60 / Ribosomal Protein S5; domain 2 - #10 ...Lon protease, AAA domain / LonB-like, AAA domain / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Helicase, Ruva Protein; domain 3 - #60 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-[(1R)-1-(DIHYDROXYBORANYL)-3-METHYLBUTYL]-L-LEUCINAMIDE / Chem-CIX / PHOSPHATE ION / endopeptidase La
Similarity search - Component
Biological speciesMeiothermus taiwanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsChang, C.I. / Kuo, C.I. / Huang, K.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors
Authors: Liao, J.H. / Ihara, K. / Kuo, C.I. / Huang, K.F. / Wakatsuki, S. / Wu, S.H. / Chang, C.I.
History
DepositionJul 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Nov 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_ref_seq_dif / 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_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: TTC1975 peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1453
Polymers80,5581
Non-polymers5862
Water6,503361
1
A: TTC1975 peptidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)486,86918
Polymers483,3506
Non-polymers3,51812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area30740 Å2
ΔGint-85 kcal/mol
Surface area138470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.995, 115.995, 136.124
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-936-

HOH

21A-953-

HOH

31A-1060-

HOH

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Components

#1: Protein TTC1975 peptidase / Lon-like protease MtaLonC


Mass: 80558.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C9DRU9, endopeptidase La
#2: Chemical ChemComp-CIX / N-[(benzyloxy)carbonyl]-L-leucyl-N-[(1R)-1-(dihydroxyboranyl)-3-methylbutyl]-L-leucinamide / MG262


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 491.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42BN3O6
References: N-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-[(1R)-1-(DIHYDROXYBORANYL)-3-METHYLBUTYL]-L-LEUCINAMIDE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10% isopropanol, 200mM di-potassium phosphate, 100mM sodium citrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.529
11K, H, -L20.471
ReflectionResolution: 2.1→50 Å / Num. all: 60538 / Num. obs: 59267 / % possible obs: 97.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 40.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 4.4 / Num. unique all: 5673 / % possible all: 94.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FW9

4fw9


Resolution: 2.19→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.699 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22675 2609 5 %RANDOM
Rwork0.17356 ---
all0.17619 50769 --
obs0.17619 49916 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.307 Å2
Baniso -1Baniso -2Baniso -3
1--16.67 Å2-0 Å2-0 Å2
2---16.67 Å2-0 Å2
3---33.34 Å2
Refinement stepCycle: LAST / Resolution: 2.19→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4471 0 40 361 4872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0194601
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3661.9896245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3295574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96422.767206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.02115732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9861548
X-RAY DIFFRACTIONr_chiral_restr0.1690.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213526
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: 2.189→2.246 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.63 160 -
Rwork0.462 3484 -
obs--94.36 %

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