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- PDB-3rzu: The Crystal Structure of the Catalytic Domain of AMSH -

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Basic information

Entry
Database: PDB / ID: 3rzu
TitleThe Crystal Structure of the Catalytic Domain of AMSH
ComponentsSTAM-binding protein
KeywordsHYDROLASE / Ubiquitin Hydrolase / STAM / Endosome-associated deubiquitinating enzyme
Function / homology
Function and homology information


hippocampal neuron apoptotic process / negative regulation of hippocampal neuron apoptotic process / deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / negative regulation of Ras protein signal transduction / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / K63-linked deubiquitinase activity / cleavage furrow / mitotic cytokinesis ...hippocampal neuron apoptotic process / negative regulation of hippocampal neuron apoptotic process / deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / negative regulation of Ras protein signal transduction / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / K63-linked deubiquitinase activity / cleavage furrow / mitotic cytokinesis / protein deubiquitination / cell surface receptor signaling pathway via JAK-STAT / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Metalloprotease DUBs / early endosome / endosome / protein domain specific binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. ...STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
STAM-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDavies, C.W. / Das, C.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural and Thermodynamic Comparison of the Catalytic Domain of AMSH and AMSH-LP: Nearly Identical Fold but Different Stability.
Authors: Davies, C.W. / Paul, L.N. / Kim, M.I. / Das, C.
History
DepositionMay 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.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_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: STAM-binding protein
B: STAM-binding protein
C: STAM-binding protein
D: STAM-binding protein
E: STAM-binding protein
F: STAM-binding protein
G: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,23121
Polymers144,3157
Non-polymers91614
Water3,117173
1
A: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7473
Polymers20,6161
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7473
Polymers20,6161
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7473
Polymers20,6161
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7473
Polymers20,6161
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7473
Polymers20,6161
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7473
Polymers20,6161
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: STAM-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7473
Polymers20,6161
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)203.491, 67.362, 113.165
Angle α, β, γ (deg.)90.00, 112.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
STAM-binding protein / Associated molecule with the SH3 domain of STAM / Endosome-associated ubiquitin isopeptidase


Mass: 20616.455 Da / Num. of mol.: 7 / Fragment: Catalytic Domain, residues 243-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMSH, STAMBP, STAMBP (AMSH) / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: O95630, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Sodium malonate, 20% PEG 3350, 5% PEG 400, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 10, 2010 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 49199 / Num. obs: 48953 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 47.5 Å2 / Rsym value: 0.085 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsDiffraction-ID% possible all
2.5-2.5932197.8
2.59-2.693.22.8199.7
2.69-2.823.44.11100
2.82-2.963.65.61100
2.96-3.153.67.51100
3.15-3.393.610.91100
3.39-3.733.613.61100
3.73-4.273.615.31100
4.27-5.383.619.6199.9
5.38-503.515.3198.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZNR

2znr


Resolution: 2.5→47.152 Å / SU ML: 0.57 / σ(F): 1.34 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 2480 5.07 %
Rwork0.1929 --
obs0.1947 48879 99 %
all-49373 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.664 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.9576 Å2-0 Å26.9534 Å2
2--1.8431 Å20 Å2
3----7.8006 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9532 0 14 173 9719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089781
X-RAY DIFFRACTIONf_angle_d1.41213300
X-RAY DIFFRACTIONf_dihedral_angle_d12.3123567
X-RAY DIFFRACTIONf_chiral_restr0.0661541
X-RAY DIFFRACTIONf_plane_restr0.0081722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54790.33941170.27762293X-RAY DIFFRACTION90
2.5479-2.59990.31611310.27262571X-RAY DIFFRACTION98
2.5999-2.65640.33061270.26122561X-RAY DIFFRACTION99
2.6564-2.71820.29911640.24652513X-RAY DIFFRACTION99
2.7182-2.78620.3151380.23232589X-RAY DIFFRACTION100
2.7862-2.86150.32071410.22892588X-RAY DIFFRACTION100
2.8615-2.94570.27251280.22792603X-RAY DIFFRACTION100
2.9457-3.04080.28731440.23462598X-RAY DIFFRACTION100
3.0408-3.14940.2771330.21752589X-RAY DIFFRACTION100
3.1494-3.27550.24691290.21632605X-RAY DIFFRACTION100
3.2755-3.42450.26711200.20452610X-RAY DIFFRACTION100
3.4245-3.6050.23361480.19492567X-RAY DIFFRACTION100
3.605-3.83080.20151370.17662625X-RAY DIFFRACTION100
3.8308-4.12640.17591460.17942604X-RAY DIFFRACTION100
4.1264-4.54140.191520.15272589X-RAY DIFFRACTION100
4.5414-5.19780.18671350.1552643X-RAY DIFFRACTION100
5.1978-6.54590.23151520.20382625X-RAY DIFFRACTION100
6.5459-47.16080.19321380.16382626X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 33.5007 Å / Origin y: 9.6836 Å / Origin z: 18.7944 Å
111213212223313233
T0.3805 Å2-0.0064 Å20.0305 Å2-0.3202 Å20.0099 Å2--0.3615 Å2
L0.4551 °2-0.0976 °20.1257 °2-0.1858 °20.0095 °2--0.3722 °2
S0.0042 Å °-0.1159 Å °0.0287 Å °0.0475 Å °0.0786 Å °0.0128 Å °0.0052 Å °-0.0105 Å °-0.08 Å °
Refinement TLS groupSelection details: all

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