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- PDB-2qz4: Human paraplegin, AAA domain in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 2qz4
TitleHuman paraplegin, AAA domain in complex with ADP
ComponentsParaplegin
KeywordsHYDROLASE / AAA+ / SPG7 / PROTEASE / ADP / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


m-AAA complex / mitochondrial protein processing / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / mitochondrial outer membrane permeabilization involved in programmed cell death / cristae formation / mitochondrial permeability transition pore complex / anterograde axonal transport / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / regulation of mitochondrial membrane permeability ...m-AAA complex / mitochondrial protein processing / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / mitochondrial outer membrane permeabilization involved in programmed cell death / cristae formation / mitochondrial permeability transition pore complex / anterograde axonal transport / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / regulation of mitochondrial membrane permeability / mitochondrial fusion / axon cytoplasm / mitochondrion organization / metalloendopeptidase activity / unfolded protein binding / nervous system development / peptidase activity / protein-containing complex assembly / mitochondrial inner membrane / mitochondrion / proteolysis / zinc ion binding / ATP binding
Similarity search - Function
Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / Helicase, Ruva Protein; domain 3 ...Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Paraplegin / Paraplegin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKarlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Karlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, I. / Kallas, A. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, J. / Sagemark, C. / Sundstrom, M. / Thorsell, A.G. / Tresauges, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2009
Title: Crystal Structure of the ATPase Domain of the Human AAA+ Protein Paraplegin/SPG7.
Authors: Karlberg, T. / van den Berg, S. / Hammarstrom, M. / Sagemark, J. / Johansson, I. / Holmberg-Schiavone, L. / Schuler, H.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Paraplegin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9792
Polymers28,5521
Non-polymers4271
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.200, 57.200, 155.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
DetailsMonomer is biological assembly

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Components

#1: Protein Paraplegin / Spastic paraplegia protein 7


Mass: 28551.885 Da / Num. of mol.: 1 / Fragment: AAA domain: Residues 305-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Brain / Gene: SPG7 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold pRARE2
References: UniProt: Q58F00, UniProt: Q9UQ90*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 100mM Bis-Tris pH 6.5, 200mM Ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2007 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 13190 / Num. obs: 13190 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.069 / Rsym value: 0.041 / Net I/σ(I): 23.7
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 7.2 / Num. unique all: 1049 / Rsym value: 0.191 / % possible all: 62.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
DNAdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CE7

2ce7


Resolution: 2.22→39.13 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 13.548 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26171 660 5 %RANDOM
Rwork0.20874 ---
obs0.21153 12529 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.905 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.22→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 27 55 1762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221734
X-RAY DIFFRACTIONr_bond_other_d0.0010.021157
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9972349
X-RAY DIFFRACTIONr_angle_other_deg0.89632821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9345219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17623.33369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17215288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2861513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021902
X-RAY DIFFRACTIONr_gen_planes_other00.02346
X-RAY DIFFRACTIONr_nbd_refined0.2320.3370
X-RAY DIFFRACTIONr_nbd_other0.2230.31203
X-RAY DIFFRACTIONr_nbtor_refined0.1830.5867
X-RAY DIFFRACTIONr_nbtor_other0.0930.5918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.3102
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0340.32
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3750.326
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.315
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.01521195
X-RAY DIFFRACTIONr_mcbond_other0.5212453
X-RAY DIFFRACTIONr_mcangle_it2.82731756
X-RAY DIFFRACTIONr_scbond_it4.1044669
X-RAY DIFFRACTIONr_scangle_it5.6276593
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.22→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 39 -
Rwork0.311 731 -
obs--100 %
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)
14.4227-0.79950.20434.3326-1.46047.205-0.25230.03790.0257-0.09450.1197-0.3562-0.90120.71910.13250.1835-0.2386-0.1639-0.0237-0.0172-0.289516.06437.6496.137
21.43910.14850.56522.4288-0.93524.4974-0.09480.0094-0.0202-0.17220.028-0.0322-0.24150.18980.06680.0476-0.0464-0.05110.02380.0117-0.26069.2629.031.692
30.6485-0.01030.89090.7792-0.47294.3444-0.0924-0.00810.09550.0613-0.05270.013-0.39370.02720.14510.026-0.0322-0.046-0.00990.0219-0.26318.93325.9329.433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA304 - 3401 - 37
2X-RAY DIFFRACTION2AA341 - 38038 - 77
3X-RAY DIFFRACTION3AA381 - 55978 - 256

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