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- PDB-5nqm: CU(I)-CSP3 (COPPER STORAGE PROTEIN 3) FROM METHYLOSINUS -

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Basic information

Entry
Database: PDB / ID: 5nqm
TitleCU(I)-CSP3 (COPPER STORAGE PROTEIN 3) FROM METHYLOSINUS
ComponentsCSP3
KeywordsCOPPER-BINDING PROTEIN / METHANE OXIDATION / COPPER STORAGE / METHANOTROPHS / PARTICULATE METHANE MONOOXYGENASE
Function / homologyUncharacterized cysteine-rich protein YhjQ-like / metal ion binding / COPPER (I) ION / CSP3
Function and homology information
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsBasle, A. / Platsaki, S. / Dennison, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K008439/1 United Kingdom
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Visualizing Biological Copper Storage: The Importance of Thiolate-Coordinated Tetranuclear Clusters.
Authors: Basle, A. / Platsaki, S. / Dennison, C.
History
DepositionApr 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.title
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: 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
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CSP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8236
Polymers14,5461
Non-polymers2775
Water68538
1
A: CSP3
hetero molecules

A: CSP3
hetero molecules

A: CSP3
hetero molecules

A: CSP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,29224
Polymers58,1834
Non-polymers1,10920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area13890 Å2
ΔGint-279 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.650, 106.680, 45.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein CSP3


Mass: 14545.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I9GEP2
#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.87 Å3/Da / Density % sol: 34.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM MgCl2, 100 mM Hepes pH 7.5, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.3746 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3746 Å / Relative weight: 1
ReflectionResolution: 1.59→45.62 Å / Num. obs: 14862 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.8
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.382 / Num. unique obs: 702 / % possible all: 99.3

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0131refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ARM

5arm


Resolution: 1.59→45.62 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.696 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20655 724 4.9 %RANDOM
Rwork0.15002 ---
obs0.1527 14138 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.412 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å20 Å2
2---0.65 Å2-0 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.59→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 5 38 978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019945
X-RAY DIFFRACTIONr_bond_other_d0.0020.02881
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9441268
X-RAY DIFFRACTIONr_angle_other_deg1.0332033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1435126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.26523.72143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98915173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2161510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021085
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02205
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_it2.1641.697504
X-RAY DIFFRACTIONr_mcbond_other2.1581.689503
X-RAY DIFFRACTIONr_mcangle_it2.522.535627
X-RAY DIFFRACTIONr_mcangle_other2.5192.537628
X-RAY DIFFRACTIONr_scbond_it3.4612.3441
X-RAY DIFFRACTIONr_scbond_other3.4572.302442
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7033.227641
X-RAY DIFFRACTIONr_long_range_B_refined3.52414.2811100
X-RAY DIFFRACTIONr_long_range_B_other3.52714.2231089
X-RAY DIFFRACTIONr_rigid_bond_restr3.29731826
X-RAY DIFFRACTIONr_sphericity_free16.344511
X-RAY DIFFRACTIONr_sphericity_bonded7.98151851
LS refinement shellResolution: 1.592→1.633 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 50 -
Rwork0.197 1025 -
obs--98.99 %

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