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- PDB-5arn: Cu(I)-CSP3 (COPPER STORAGE PROTEIN 3) FROM METHYLOSINUS -

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Basic information

Entry
Database: PDB / ID: 5arn
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVita, N. / Landolfi, G. / Basle, A. / Platsaki, S. / Waldron, K. / Dennison, C.
CitationJournal: To be Published
Title: Novel Cytosolic Copper Storage Proteins
Authors: Vita, N. / Landolfi, G. / Basle, A. / Platsaki, S. / Waldron, K. / Dennison, C.
History
DepositionSep 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_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: CSP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,75320
Polymers14,5461
Non-polymers1,20719
Water905
1
A: CSP3
hetero molecules

A: CSP3
hetero molecules

A: CSP3
hetero molecules

A: CSP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,01380
Polymers58,1834
Non-polymers4,82976
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area20100 Å2
ΔGint-1018.9 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.902, 105.902, 45.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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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 (bacteria) / Strain: OB3B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1I9GEP2*PLUS
#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 75 MM MGCL2, 100 MM HEPES PH 7.5, AND 34% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.377
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.377 Å / Relative weight: 1
ReflectionResolution: 2.3→41.91 Å / Num. obs: 5998 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5ARM

5arm


Resolution: 2.3→74.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.987 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 13-19 AND 75-80 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.24274 306 5.2 %RANDOM
Rwork0.18573 ---
obs0.18912 5534 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.733 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2--2.14 Å20 Å2
3----4.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→74.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 19 5 862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019843
X-RAY DIFFRACTIONr_bond_other_d0.0020.02778
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9391133
X-RAY DIFFRACTIONr_angle_other_deg1.02531783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6885113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73123.23534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79215144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.265158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02961
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02183
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_it3.5344.992461
X-RAY DIFFRACTIONr_mcbond_other3.5344.988460
X-RAY DIFFRACTIONr_mcangle_it4.8767.47571
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1025.462381
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 20 -
Rwork0.246 381 -
obs--93.47 %

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