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- PDB-2cki: Structure of Ulilysin, a member of the pappalysin family of metzi... -

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Basic information

Entry
Database: PDB / ID: 2cki
TitleStructure of Ulilysin, a member of the pappalysin family of metzincin metalloendopeptidases.
ComponentsULILYSIN
KeywordsHYDROLASE / METALLOPROTEASE
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 / MAD / Resolution: 1.7 Å
AuthorsTallant, C. / Garcia-Castellanos, R. / Seco, J. / Baumann, U. / Gomis-Ruth, F.X.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Molecular Analysis of Ulilysin, the Structural Prototype of a New Family of Metzincin Metalloproteases.
Authors: Tallant, C. / Garcia-Castellanos, R. / Seco, J. / Baumann, U. / Gomis-Ruth, F.X.
History
DepositionApr 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 14, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._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_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
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ULILYSIN
B: ULILYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,03519
Polymers58,5672
Non-polymers1,46817
Water10,755597
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-139.5 kcal/mol
Surface area21150 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-128.6 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.564, 126.148, 87.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

21B-2038-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A61 - 322
2112B61 - 322
1212A401 - 402
2212B401 - 402

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ULILYSIN


Mass: 29283.436 Da / Num. of mol.: 2 / Fragment: RESIDUES 61-322 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: EACH CHAIN FURTHER INCLUDES 1 ZN (999) AND 2 CA (998,997). DIPEPTIDE ARG401-VAL402 IN EACH ACTIVE SITE. PROBABLY PICKED UP BY THE ACTIVE-SITE POCKETS DURING PURIFICATION/ CRYSTALLISATION
Source: (gene. exp.) METHANOSARCINA ACETIVORANS (archaea) / Strain: C2A / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8TL28

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Non-polymers , 6 types, 614 molecules

#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 269 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 269 TO ALA
Sequence detailsC269A MUTATION.

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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: 2.4 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: EQUIVOLUMETRIC SITTING DROPS CONSISTING OF PROTEIN (5 MG PER ML IN 30MM TRIS PH 7.5, 2MM DTT, 100MM NACL) AND RESERVOIR SOLUTION (18% PEG 8000, 0.1M MES PH6.5, 0.2M CACL2) AFTER SEVERAL ...Details: EQUIVOLUMETRIC SITTING DROPS CONSISTING OF PROTEIN (5 MG PER ML IN 30MM TRIS PH 7.5, 2MM DTT, 100MM NACL) AND RESERVOIR SOLUTION (18% PEG 8000, 0.1M MES PH6.5, 0.2M CACL2) AFTER SEVERAL WEEKS AT 20 DEGREES CELCIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.984
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.7→39 Å / Num. obs: 61061 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→39 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.32 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 610 1 %RANDOM
Rwork0.173 ---
obs0.174 60401 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.89 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 79 597 4754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224264
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.925804
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2425.094212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54115652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7061520
X-RAY DIFFRACTIONr_chiral_restr0.0920.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023312
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21960
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23025
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2491
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9121.52688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25524279
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.34231781
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5274.51525
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1056tight positional0.030.05
2B1056tight positional0.030.05
1A997medium positional0.250.5
2B997medium positional0.250.5
1A1056tight thermal0.120.5
2B1056tight thermal0.120.5
1A997medium thermal0.472
2B997medium thermal0.472
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 63
Rwork0.235 4367
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)
10.9171-0.24290.38520.5088-0.05240.9185-0.03450.11770.048-0.0502-0.0021-0.0501-0.0854-0.00870.0365-0.078-0.0082-0.0062-0.09460.0206-0.062215.463947.5442-22.3466
21.0103-0.23350.39610.6004-0.18661.3002-0.01340.12210.0678-0.0554-0.0105-0.043-0.0662-0.01220.0239-0.0624-0.00670-0.09120.016-0.054415.492447.4038-22.2997
35.01870.01545.071500.01565.12490.26610.7379-1.0935-2.04910.8232-0.4561-0.7902-0.7605-1.0893-0.00690.0034-0.0051-0.00130.0009-0.003120.166342.3717-29.137
40.7169-0.0979-0.54090.42060.0441.0958-0.03360.1541-0.0499-0.0335-0.01220.01610.0889-0.07070.0458-0.0748-0.0168-0.0006-0.0612-0.0293-0.05959.343815.873-22.6469
50.8359-0.1461-0.56040.47830.21391.4734-0.03340.1677-0.0728-0.036-0.00990.02330.0681-0.05880.0433-0.0639-0.02190.0001-0.0545-0.0243-0.04899.308116.0159-22.5837
61.7170.0375-1.16550.0008-0.02550.79120.06670.32110.7535-1.37050.25520.4506-0.0919-1.1891-0.3219-0.0051-0.00140.0036-0.00020.0002-0.00184.671821.164-29.3503
70.3253-0.0709-0.03060.4520.00380.3619-0.01840.08220.00290.0056-0.0134-0.0063-0.0158-0.02420.03180.0279-0.0051-0.00420.0571-0.00330.038112.301132.5185-20.788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 322
2X-RAY DIFFRACTION2A997 - 999
3X-RAY DIFFRACTION3A401 - 402
4X-RAY DIFFRACTION4B61 - 322
5X-RAY DIFFRACTION5B997 - 999
6X-RAY DIFFRACTION6B401 - 402
7X-RAY DIFFRACTION7A2001 - 2305
8X-RAY DIFFRACTION7B2001 - 2292

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