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- PDB-3amj: The crystal structure of the heterodimer of M16B peptidase from S... -

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Basic information

Entry
Database: PDB / ID: 3amj
TitleThe crystal structure of the heterodimer of M16B peptidase from Sphingomonas sp. A1
Components
  • zinc peptidase active subunit
  • zinc peptidase inactive subunit
KeywordsHYDROLASE / alpha/beta / zinc peptidase / zinc binding
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / catalytic activity / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc peptidase inactive subunit / Zinc peptidase active subunit
Similarity search - Component
Biological speciesSphingomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMaruyama, Y. / Chuma, A. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Heterosubunit composition and crystal structures of a novel bacterial M16B metallopeptidase
Authors: Maruyama, Y. / Chuma, A. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionAug 20, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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_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
B: zinc peptidase inactive subunit
C: zinc peptidase active subunit
D: zinc peptidase inactive subunit
A: zinc peptidase active subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,7356
Polymers188,6054
Non-polymers1312
Water1,08160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-26 kcal/mol
Surface area64430 Å2
MethodPISA
2
B: zinc peptidase inactive subunit
A: zinc peptidase active subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3683
Polymers94,3022
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-15 kcal/mol
Surface area32310 Å2
MethodPISA
3
C: zinc peptidase active subunit
D: zinc peptidase inactive subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3683
Polymers94,3022
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-7 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.457, 100.676, 253.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHOR DEFINED BIOLOGICAL UNIT: UNKNOWN. AUTHOR STATED THAT GEL FILTRATION COLUMN CHROMATOGRAPHY SUGGESTED A HETERO-TETRAMER, AND NATIVE PAGE SUGGESTED HETERO-DIMERS.

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Components

#1: Protein zinc peptidase inactive subunit


Mass: 45902.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas (bacteria) / Strain: sp. A1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: F2Z283*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein zinc peptidase active subunit


Mass: 48399.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas (bacteria) / Strain: sp. A1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: F2Z284*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCES OF THE PROTEINS HAVE BEEN DEPOSITED TO DDBJ, BUT ARE NOT PUBLICLY AVAILABLE AT THE ...THE SEQUENCES OF THE PROTEINS HAVE BEEN DEPOSITED TO DDBJ, BUT ARE NOT PUBLICLY AVAILABLE AT THE TIME OF PROCESSING.

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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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 10% PDG 8000, 0.1M Tris-HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 35597 / % possible obs: 99.9 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 23.79
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 7.7 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GWD

3gwd


Resolution: 3→33.76 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.792 / SU B: 54.019 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.567 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30046 1777 5 %RANDOM
Rwork0.21035 ---
obs0.21486 33717 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.149 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 3→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12829 0 2 60 12891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02213073
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.9617747
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03351665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76123.244598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.042152144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.64615126
X-RAY DIFFRACTIONr_chiral_restr0.0720.21999
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110018
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_it0.351.58291
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.678213282
X-RAY DIFFRACTIONr_scbond_it0.96534782
X-RAY DIFFRACTIONr_scangle_it1.7364.54465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 135 -
Rwork0.272 2433 -
obs--99.77 %
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)
10.66720.1902-0.00120.3942-0.11480.39980.0412-0.02170.06190.0733-0.02480.0669-0.00480.0046-0.01640.06940.00050.02050.0371-0.01860.0201-14.8118-0.589192.9306
20.13760.07970.09341.11450.12020.5894-0.01130.02960.0169-0.0390.0403-0.0073-0.0099-0.0255-0.0290.00710.0150.00040.07490.01270.0096-23.6913-3.111831.2757
31.00190.48730.13171.52630.05570.1178-0.03280.1714-0.3343-0.08260.0962-0.3774-0.0542-0.0194-0.06340.03070.0160.02730.05-0.05770.1524-11.78840.70431.8756
40.48530.2682-0.25480.4693-0.25340.4853-0.02870.0386-0.0487-0.00680.0193-0.02660.0174-0.00190.00950.03520.0047-0.00120.03740.00360.046-10.5982-14.584467.7439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B21 - 434
2X-RAY DIFFRACTION2C29 - 450
3X-RAY DIFFRACTION3D21 - 431
4X-RAY DIFFRACTION4A1 - 488

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