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

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Basic information

Entry
Database: PDB / ID: 3wkm
TitleThe periplasmic PDZ tandem fragment of the RseP homologue from Aquifex aeolicus in complex with the Fab fragment
Components
  • MOUSE IGG1-KAPPA FAB (HEAVY CHAIN)
  • MOUSE IGG1-KAPPA FAB (LIGHT CHAIN)
  • Putative 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative zinc metalloprotease aq_1964
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative zinc metalloprotease aq_1964
H: MOUSE IGG1-KAPPA FAB (HEAVY CHAIN)
L: MOUSE IGG1-KAPPA FAB (LIGHT CHAIN)
B: Putative zinc metalloprotease aq_1964
I: MOUSE IGG1-KAPPA FAB (HEAVY CHAIN)
M: MOUSE IGG1-KAPPA FAB (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)136,6926
Polymers136,6926
Non-polymers00
Water6,972387
1
A: Putative zinc metalloprotease aq_1964
H: MOUSE IGG1-KAPPA FAB (HEAVY CHAIN)
L: MOUSE IGG1-KAPPA FAB (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)68,3463
Polymers68,3463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-33 kcal/mol
Surface area27370 Å2
MethodPISA
2
B: Putative zinc metalloprotease aq_1964
I: MOUSE IGG1-KAPPA FAB (HEAVY CHAIN)
M: MOUSE IGG1-KAPPA FAB (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)68,3463
Polymers68,3463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-28 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.243, 86.042, 92.542
Angle α, β, γ (deg.)100.84, 96.92, 101.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative zinc metalloprotease aq_1964


Mass: 19997.455 Da / Num. of mol.: 2 / 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
#2: Antibody MOUSE IGG1-KAPPA FAB (HEAVY CHAIN)


Mass: 24268.041 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#3: Antibody MOUSE IGG1-KAPPA FAB (LIGHT CHAIN)


Mass: 24080.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsDNA SEQUENCEs FOR CHAIN H, I, L AND M WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE ...DNA SEQUENCEs FOR CHAIN H, I, L AND M WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. DNA SEQUENCE FOR CHAINS H AND I HAS DDBJ ACCESSION NUMBER AB701676. DNA SEQUENCE FOR CHAINS L AND M HAS DDBJ ACCESSION NUMBER AB701677.

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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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growpH: 7
Details: 16%(W/V) POLYETHYLENE GLYCOL 8000, 200MM SODIUM MALONATE, 0.5%(W/) N-OCTYL BETA-D-GLUCOPYRANOSIDE, PH 7.0, VAPOR DIFFUSION, SITTING 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: Jun 10, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.44 Å / Num. obs: 74923 / % possible obs: 98.2 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.32 Å / % possible all: 97.2

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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: 1NSN

1nsn


Resolution: 2.2→47.44 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.989 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3771 5 %RANDOM
Rwork0.224 ---
obs0.227 74918 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-0.73 Å20.33 Å2
2---0.61 Å20.17 Å2
3---2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9228 0 0 387 9615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.029627
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.96713112
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77551223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25924.741386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.072151643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5611541
X-RAY DIFFRACTIONr_chiral_restr0.0740.21474
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217233
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: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 283 -
Rwork0.302 5255 -
obs--97.09 %

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