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- PDB-2j83: Ulilysin metalloprotease in complex with batimastat. -

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Basic information

Entry
Database: PDB / ID: 2j83
TitleUlilysin metalloprotease in complex with batimastat.
ComponentsULILYSIN
KeywordsHYDROLASE / IGFBP PROTEASE / METALLOPROTEASE / HYDROXAMATE INHIBITOR / CANCER / METZINCIN
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
Biological speciesMETHANOSARCINA ACETIVORANS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarcia-Castellanos, R. / Tallant, C. / Marrero, A. / Sola, M. / Baumann, U. / Gomis-Ruth, F.X.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2007
Title: Substrate Specificity of a Metalloprotease of the Pappalysin Family Revealed by an Inhibitor and a Product Complex.
Authors: Garcia-Castellanos, R. / Tallant, C. / Marrero, A. / Sola, M. / Baumann, U. / Gomis-Ruth, F.X.
#1: Journal: 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
DepositionOct 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 18, 2015Group: Data collection / Non-polymer description
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)59,81115
Polymers58,1562
Non-polymers1,65513
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-133.5 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.850, 60.730, 168.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILELEULEU5AA64 - 3214 - 261
21ILEILELEULEU5BB64 - 3214 - 261
12BATBATBATBAT1AC996
22BATBATBATBAT1BI996

NCS oper: (Code: given
Matrix: (-0.97251, -0.04123, -0.2292), (0.04729, -0.99866, -0.021), (-0.22803, -0.03126, 0.97315)
Vector: 90.198, 85.5975, 11.59586)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ULILYSIN


Mass: 29078.186 Da / Num. of mol.: 2 / Fragment: ACTIVE CATALYTIC DOMAIN, RESIDUES 61-322 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA ACETIVORANS (archaea) / Strain: C2A
Description: M.ACETIVORANS TOTAL DNA WAS OBTAINED FORM THE GERMAN COLLECTION OF MICROORGANISMS (DSM).
Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8TL28

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Non-polymers , 5 types, 476 molecules

#2: Chemical ChemComp-BAT / 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE / BATIMASTAT / BB94 / Batimastat


Mass: 477.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H31N3O4S2 / Comment: inhibitor*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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 detailsMUTANT C269A.

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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: 2.6 Å3/Da / Density % sol: 53 %
Description: THE PRESENT INHIBITOR COMPLEX CRYSTALS WERE ISOMORPHOUS TO THOSE OF THE STARTING MODEL.
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: VAPOUR-DIFFUSION CRYSTALLISATION METHOD FROM SITTING DROPS CONSISTING OF 1 MICROLITER OF PROULILYSIN (5 MG/ML IN 30MM TRIS-HCL PH 7.5, 2MM DITHIOTHREITOL, 100MM NACL), 1 MICROLITER OF ...Details: VAPOUR-DIFFUSION CRYSTALLISATION METHOD FROM SITTING DROPS CONSISTING OF 1 MICROLITER OF PROULILYSIN (5 MG/ML IN 30MM TRIS-HCL PH 7.5, 2MM DITHIOTHREITOL, 100MM NACL), 1 MICROLITER OF RESERVOIR SOLUTION (18% PEG 8000, 0.1M 2-MORPHOLINOETHANESULFONIC ACID, PH6.5, 0.2M CACL2) AND, OPTIONALLY, 0.2 MICROLITER OF 0.1M SPERMIDINE OR 30% 2, 4-METHYLPENTANEDIOL AS ADDITIVES.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→45.6 Å / Num. obs: 154616 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 13.9 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CKI

2cki


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.695 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THERE IS NCS RELATING CHAINS A AND B (180.1 DEGREES AROUND A ROTATION AXIS DEFINED BY THE DIRECTION COSINES 0.002,MINUS 0.011, MINUS 1.000, I.E. ALMOST PARALLEL TO CELL AXIS C).
RfactorNum. reflection% reflectionSelection details
Rfree0.211 520 1.3 %RANDOM
Rwork0.161 ---
obs0.161 39606 96.4 %-
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: 17 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2--3.05 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 95 463 4596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224242
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9515777
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00325.359209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97815625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8411516
X-RAY DIFFRACTIONr_chiral_restr0.080.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023317
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.21980
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22963
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2401
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3841.52636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6824193
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.20431816
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9274.51584
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
32tight positional0.030.05
1032medium positional0.150.5
966loose positional0.385
32tight thermal0.10.5
1032medium thermal0.482
966loose thermal0.9410
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.216 38
Rwork0.163 2628
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)
10.5834-0.02950.25190.8130.48111.9570.02930.02580.00970.0039-0.02920.01150.0319-0.0673-0.0002-0.0860.00670.0034-0.07030.0054-0.03817.748247.3703102.8945
20.80590.0954-0.48510.4912-0.30191.71130.01090.007-0.01980.03290.01170.00380.05170.0092-0.0226-0.0570.00850.0014-0.0935-0.0021-0.039347.376136.9575106.1865
30.7268-0.0854-0.02180.17960.11950.30020.01380.03860.01340.003-0.02180.003-0.0112-0.00650.0080.05960.00190.0045-0.05180.00550.037334.062242.5804102.9085
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A63 - 321
2X-RAY DIFFRACTION1A997 - 999
3X-RAY DIFFRACTION2B63 - 321
4X-RAY DIFFRACTION2B997 - 999
5X-RAY DIFFRACTION3A2001 - 2220
6X-RAY DIFFRACTION3B2001 - 2243
7X-RAY DIFFRACTION3A996
8X-RAY DIFFRACTION3B996

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