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- PDB-3wkl: The periplasmic PDZ tandem fragment of the RseP homologue from Aq... -

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Basic information

Entry
Database: PDB / ID: 3wkl
TitleThe periplasmic PDZ tandem fragment of the RseP homologue from Aquifex aeolicus
ComponentsPutative Zinc Metalloprotease AQ_1964
KeywordsHYDROLASE / PDZ DOMAIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M50, putative membrane-associated zinc metallopeptidase / Peptidase M50 / Peptidase family M50 / PDZ domain / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Peptidase M50, putative membrane-associated zinc metallopeptidase / Peptidase M50 / Peptidase family M50 / PDZ domain / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Mainly Beta
Similarity search - Domain/homology
Putative zinc metalloprotease aq_1964
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNogi, T. / Tabata, S. / Tamura-kawakami, K. / Takagi, J.
CitationJournal: Structure / Year: 2013
Title: A Structure-Based Model of Substrate Discrimination by a Noncanonical PDZ Tandem in the Intramembrane-Cleaving Protease RseP
Authors: Hizukuri, Y. / Oda, T. / Tabata, S. / Tamura-kawakami, K. / Oi, R. / Sato, M. / Takagi, J. / Akiyama, Y. / Nogi, T.
History
DepositionOct 28, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Zinc Metalloprotease AQ_1964


Theoretical massNumber of molelcules
Total (without water)19,9971
Polymers19,9971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.861, 78.861, 211.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Putative Zinc Metalloprotease AQ_1964


Mass: 19997.455 Da / Num. of mol.: 1 / Fragment: PDZ TANDEM FRAGMENT, UNP RESIDUES 115-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Strain: VF5 / Gene: AQ_1964 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O67776, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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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: 4.75 Å3/Da / Density % sol: 74.13 %
Crystal growpH: 4.5
Details: 1.5M AMMONIUM SULFATE, 0.1M SODIUM ACCETATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 21, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.1 Å / Num. obs: 10257 / % possible obs: 99.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.8→2.95 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZPL, 2ZPM

2zpl

2zpm


Resolution: 2.8→39.44 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.077 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.295 520 5.1 %RANDOM
Rwork0.255 ---
obs0.257 10240 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å21.61 Å20 Å2
2--3.21 Å20 Å2
3----4.82 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 0 0 1409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191432
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2532.0121930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7315179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54525.28353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8915288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.25157
X-RAY DIFFRACTIONr_chiral_restr0.0690.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211026
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.8→2.95 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.41 77 -
Rwork0.346 1122 -
obs--99.17 %

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