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- PDB-1z0w: Crystal Structure of A. fulgidus Lon proteolytic domain at 1.2A r... -

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Basic information

Entry
Database: PDB / ID: 1z0w
TitleCrystal Structure of A. fulgidus Lon proteolytic domain at 1.2A resolution
ComponentsPutative protease La homolog type
KeywordsHYDROLASE / ATP-DEPENDENT PROTEASE / CATALYTIC SER-LYS DYAD / B-type Lon
Function / homology
Function and homology information


ATP-dependent peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / protein catabolic process / serine-type endopeptidase activity / regulation of DNA-templated transcription / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
Lon protease, archaeal / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease ...Lon protease, archaeal / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Archaeal Lon protease
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsBotos, I. / Melnikov, E.E. / Cherry, S. / Kozlov, S. / Makhovskaya, O.V. / Tropea, J.E. / Gustchina, A. / Rotanova, T.V. / Wlodawer, A.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Atomic-resolution Crystal Structure of the Proteolytic Domain of Archaeoglobus fulgidus Lon Reveals the Conformational Variability in the Active Sites of Lon Proteases
Authors: Botos, I. / Melnikov, E.E. / Cherry, S. / Kozlov, S. / Makhovskaya, O.V. / Tropea, J.E. / Gustchina, A. / Rotanova, T.V. / Wlodawer, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Pathological crystallography: case studies of several unusual macromolecular crystals
Authors: Dauter, Z. / Botos, I. / LaRonde-LeBlanc, N. / Wlodawer, A.
History
DepositionMar 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Putative protease La homolog type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1993
Polymers22,1181
Non-polymers802
Water4,107228
1
A: Putative protease La homolog type
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)133,19218
Polymers132,7116
Non-polymers48112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+5/61
crystal symmetry operation2_555-y,x-y,z+2/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation3_555-x+y,-x,z+1/31
crystal symmetry operation5_555y,-x+y,z+1/61
Unit cell
Length a, b, c (Å)84.470, 84.470, 41.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Putative protease La homolog type


Mass: 22118.484 Da / Num. of mol.: 1 / Fragment: proteolytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pJT4 / Production host: Escherichia coli (E. coli) / References: UniProt: O29883, endopeptidase La
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 1.94 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000,MES,calcium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. all: 52481 / Num. obs: 52481 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.6
Reflection shellResolution: 1.15→1.24 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 3.1 / % possible all: 94.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.2→20 Å / Num. parameters: 15941 / Num. restraintsaints: 19071 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.8%
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 2619 5.1 %RANDOM
Rwork0.1372 ---
all0.1372 52481 --
obs0.1372 51579 97.5 %-
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 1537 / Occupancy sum non hydrogen: 1751.47
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 0 2 228 1770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0296
X-RAY DIFFRACTIONs_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.027
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0.088

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