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- PDB-3zuk: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTE... -

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Basic information

Entry
Database: PDB / ID: 3zuk
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE ZMP1 IN COMPLEX WITH INHIBITOR
ComponentsENDOPEPTIDASE, PEPTIDASE FAMILY M13
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / PATHOGENICITY / PHAGOSOME MATURATION
Function / homology
Function and homology information


peptidoglycan-based cell wall / metalloendopeptidase activity / protein processing / metal ion binding / plasma membrane
Similarity search - Function
Neutral endopeptidase; domain 2 / Neutral endopeptidase , domain2 / Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Neprilysin-like (M13) protease domain profile. / Collagenase (Catalytic Domain) ...Neutral endopeptidase; domain 2 / Neutral endopeptidase , domain2 / Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Neprilysin-like (M13) protease domain profile. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHORAMIDON / 2,2',2''-NITRILOTRIETHANOL / ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-RDF / Endopeptidase, peptidase family M13
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFerraris, D.M. / Sbardella, D. / Petrera, A. / Marini, S. / Amstutz, B. / Coletta, M. / Sander, P. / Rizzi, M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of Mycobacterium Tuberculosis Zinc-Dependent Metalloprotease-1 (Zmp1), a Metalloprotease Involved in Pathogenicity.
Authors: Ferraris, D.M. / Sbardella, D. / Petrera, A. / Marini, S. / Amstutz, B. / Coletta, M. / Sander, P. / Rizzi, M.
History
DepositionJul 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Mar 6, 2013Group: Other
Revision 1.3Dec 20, 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_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_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: ENDOPEPTIDASE, PEPTIDASE FAMILY M13
B: ENDOPEPTIDASE, PEPTIDASE FAMILY M13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,28572
Polymers156,2662
Non-polymers8,01970
Water5,981332
1
A: ENDOPEPTIDASE, PEPTIDASE FAMILY M13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,95133
Polymers78,1331
Non-polymers3,81832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDOPEPTIDASE, PEPTIDASE FAMILY M13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,33439
Polymers78,1331
Non-polymers4,20138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.290, 198.770, 63.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ENDOPEPTIDASE, PEPTIDASE FAMILY M13 / PROBABLE ZINC METALLOPROTEASE / ZMP1 METALLOPROTEASE


Mass: 78132.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET100D/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O53649, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 11 types, 402 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-RDF / N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN / PHOSPHORAMIDON


Type: peptide-like, Glycopeptide / Class: Enzyme inhibitor / Mass: 543.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H34N3O10P / References: PHOSPHORAMIDON / Comment: inhibitor*YM
#4: Chemical ChemComp-211 / 2,2',2''-NITRILOTRIETHANOL


Mass: 149.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO3
#5: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTRIETHANOLAMINE (211): POSSIBLE CONTAMINANT OF THE PHOSPHORAMIDON PREPARATION PHOSPHORAMIDON (RDF): ...TRIETHANOLAMINE (211): POSSIBLE CONTAMINANT OF THE PHOSPHORAMIDON PREPARATION PHOSPHORAMIDON (RDF): ZMP1 INHIBITOR ACETATE (ACT): COMPONENT OF THE CRYSTALLIZATION BUFFER ZINC (ZN): CATALYTICALLY ESSENTIAL ZINC ION POLYETHYLENE GLYCOL (PEG): COMPONENT OF THE CRYSTALLIZATION BUFFER SULFATE (SO4): COMPONENT OF THE CRYSTALLIZATION BUFFER POLYETHYLENE GLYCOL (PG4): COMPONENT OF THE CRYSTALLIZATION BUFFER POLYETHYLENE GLYCOL (PGE): COMPONENT OF THE CRYSTALLIZATION BUFFER
Sequence detailsTHE CRYSTALLIZED PROTEIN CONTAINS THE N-TERMINAL TAG MRGSHHHHHHGMASMTGGQQMGRDLYDDDDKDHPFT

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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: 2.7 Å3/Da / Density % sol: 54.9 % / Description: NONE
Crystal growpH: 4.6
Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE, PH 4.6, 30% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.99
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 48222 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / % possible all: 75.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DMT

1dmt


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.875 / SU B: 19.929 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 1.443 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE OMITTED FROM THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.24964 938 2 %RANDOM
Rwork0.17509 ---
obs0.17661 46070 92.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 514 332 11220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02111084
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.96414932
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70651310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95823.333558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.195151614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.96715100
X-RAY DIFFRACTIONr_chiral_restr0.1030.21552
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218532
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_it0.6031.56567
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.157210454
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9534517
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1784.54478
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
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 48 -
Rwork0.206 2368 -
obs--65.88 %
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)
10.67340.1528-0.10691.6429-0.55320.74610.0213-0.0052-0.1263-0.01730.05680.18780.0906-0.0717-0.07810.0652-0.0271-0.01510.03250.01480.054658.060363.056812.3024
21.63290.1676-0.48250.48890.01180.5275-0.0295-0.00880.1155-0.02160.0146-0.05330.02520.0430.01490.05630.0075-0.02050.06650.01670.0405100.188791.763531.5911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 663
2X-RAY DIFFRACTION2B39 - 663

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