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- PDB-3lun: Structure of ulilysin mutant M290C -

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Basic information

Entry
Database: PDB / ID: 3lun
TitleStructure of ulilysin mutant M290C
ComponentsUlilysin
KeywordsHYDROLASE / metallopeptidase / metal ion binding / calcium ion binding / Calcium / Disulfide bond / Metal-binding / Metalloprotease / Protease / Zinc / Zymogen
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M43, pregnancy-associated plasma-A / Pregnancy-associated plasma protein-A / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / VALINE / Ulilysin
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTallant, C. / Garcia-Castellanos, R. / Baumann, U. / Gomis-Ruth, F.X.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: On the relevance of the Met-turn methionine in metzincins.
Authors: Tallant, C. / Garcia-Castellanos, R. / Baumann, U. / Gomis-Ruth, F.X.
History
DepositionFeb 18, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ulilysin
B: Ulilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,04416
Polymers58,0122
Non-polymers1,03214
Water10,377576
1
A: Ulilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2846
Polymers29,0061
Non-polymers2785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ulilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,76010
Polymers29,0061
Non-polymers7549
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-15 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.510, 116.290, 164.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ulilysin


Mass: 29006.080 Da / Num. of mol.: 2 / Fragment: UNP residues 61-322 / Mutation: M290C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: MA_3214 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TL28, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 6 types, 590 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#6: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7 / Details: pH 7, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→47.5 Å / Num. obs: 52160 / Redundancy: 8.1 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.018 / Net I/σ(I): 28.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 10.9 / Num. unique all: 52160 / Rsym value: 0.018

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.5.0102refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CKI

2cki


Resolution: 1.8→39.93 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.442 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 464 0.9 %RANDOM
Rwork0.16085 ---
obs0.16128 51696 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.743 Å2
Baniso -1Baniso -2Baniso -3
1-2.97 Å20 Å20 Å2
2---1.26 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4028 0 51 576 4655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224176
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9335694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50625.311209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17215627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6311517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213273
X-RAY DIFFRACTIONr_mcbond_it0.841.52589
X-RAY DIFFRACTIONr_mcangle_it1.49524205
X-RAY DIFFRACTIONr_scbond_it2.50131587
X-RAY DIFFRACTIONr_scangle_it3.944.51489
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 26 -
Rwork0.173 3673 -
obs--95.58 %

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