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- PDB-9ggo: Strand-swapped dimer of engineered copper binding SH3-like protein -

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Basic information

Entry
Database: PDB / ID: 9ggo
TitleStrand-swapped dimer of engineered copper binding SH3-like protein
ComponentsSH3-like protein
KeywordsMETAL BINDING PROTEIN / protein design / metal binding site / SH3-like domain
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchwan, M. / Kopp, J. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586-6 Germany
CitationJournal: Acs Cent.Sci. / Year: 2025
Title: Strand-Swapped SH3 Domain Dimer with Superoxide Dismutase Activity.
Authors: Hage, F.R. / Schwan, M. / Conde Gonzalez, M.R. / Huber, J. / Germer, S. / Macri, M. / Kopp, J. / Sinning, I. / Thomas, F.
History
DepositionAug 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SH3-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0655
Polymers6,8141
Non-polymers2514
Water36020
1
A: SH3-like protein
hetero molecules

A: SH3-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,13010
Polymers13,6272
Non-polymers5028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area6340 Å2
ΔGint-61 kcal/mol
Surface area6930 Å2
Unit cell
Length a, b, c (Å)56.509, 56.509, 58.778
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein SH3-like protein


Mass: 6813.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.98 Å3/Da / Density % sol: 69.06 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Reservoir: 1.26 M ammonium sulfate, 0.1 M CHES pH 9.5, 0.2 M sodium chloride. Drops contained 300 nL reservoir solution and 300 nL concentrated protein.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.3694 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 23, 2023
RadiationMonochromator: Si(1,1,1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3694 Å / Relative weight: 1
ReflectionResolution: 2→37.61 Å / Num. obs: 15348 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 37.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.038 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 2.814 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1092 / CC1/2: 0.833 / Rpim(I) all: 0.653 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDS20230630data reduction
Aimless1.12.16data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.61 Å / SU ML: 0.1802 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.5019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 705 4.98 %
Rwork0.2034 13463 -
obs0.2046 14168 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.01 Å2
Refinement stepCycle: LAST / Resolution: 2→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms481 0 10 20 511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004497
X-RAY DIFFRACTIONf_angle_d0.6403664
X-RAY DIFFRACTIONf_chiral_restr0.043668
X-RAY DIFFRACTIONf_plane_restr0.004887
X-RAY DIFFRACTIONf_dihedral_angle_d15.2028190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.35321100.33752741X-RAY DIFFRACTION99.76
2.16-2.370.30571860.30942640X-RAY DIFFRACTION99.89
2.37-2.710.32111660.27592689X-RAY DIFFRACTION99.93
2.72-3.420.19251140.20932688X-RAY DIFFRACTION99.64
3.42-37.610.18441290.152705X-RAY DIFFRACTION99.68
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)
10.138643496107-0.144516472881-0.0971875326740.1520402577550.116538210770.7959112166480.0603125428163-0.2682309279320.06057294993410.0159615524724-0.01449752245320.0918878497902-0.37363907247-0.673267350963-0.001477318713790.326387855014-0.008357127340470.02085351916430.390324728277-0.03164856182030.407593892757-26.619958999617.1319219306-17.1182968073
20.1806285065060.128497177194-0.05801865891390.104585271857-0.06302467709020.05183398072410.2112242702950.2175428494710.128973751538-0.1283112703150.153452019009-0.253767375505-0.04876514038560.107806076292-0.0009342537253120.6078394733150.01759868347530.12180739720.593068107118-0.0007478634527440.570624185069-10.476329185612.8861656145-21.8796675363
30.1485328737320.104574182534-0.1763989897390.0753424326911-0.1154251848290.2069886265-0.01666108922770.4237261819970.00257472704691-0.1695811310070.0946509642306-0.01319087318150.0716724090678-0.0950224704354-0.0001262839685510.367256003734-0.0573761221647-0.00142478688990.4778516840530.01808113910.39664457091-3.7344375810827.738567816-26.0332933966
40.172191299784-0.01233760232520.1050384990710.3346269045610.07576521407270.279844888454-0.0442645813601-0.05915836766380.1383560360270.136346338616-0.0786931150476-0.0462922660002-0.194301274346-0.0141206493853-0.0003065522379180.4023203354990.00492116182514-0.004620795443110.4547724772120.04770092532850.345329406164-21.117408110819.5280565992-16.850333058
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 11 )1 - 111 - 11
22chain 'A' and (resid 12 through 16 )12 - 1612 - 16
33chain 'A' and (resid 17 through 31 )17 - 3117 - 31
44chain 'A' and (resid 32 through 58 )32 - 5832 - 58

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