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- PDB-5arm: APO-CSP3 (COPPER STORAGE PROTEIN 3) FROM METHYLOSINUS -

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Basic information

Entry
Database: PDB / ID: 5arm
TitleAPO-CSP3 (COPPER STORAGE PROTEIN 3) FROM METHYLOSINUS
ComponentsCSP3
KeywordsCOPPER-BINDING PROTEIN / COPPER BINDING PROTEIN / METHANE OXIDATION / COPPER STORAGE / METHANOTROPHS / PARTICULATE METHANE MONOOXYGENASE
Function / homologyUncharacterized cysteine-rich protein YhjQ-like / metal ion binding / CSP3
Function and homology information
Biological speciesMETHYLOSINUS TRICHOSPORIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.194 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CSP3


Theoretical massNumber of molelcules
Total (without water)14,5461
Polymers14,5461
Non-polymers00
Water1,47782
1
A: CSP3

A: CSP3

A: CSP3

A: CSP3


Theoretical massNumber of molelcules
Total (without water)58,1834
Polymers58,1834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation2_655-x+1,-y,z1
Buried area11660 Å2
ΔGint-81 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.170, 105.500, 45.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1024-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.95 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growDetails: 40% PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 100 MM HEPES PH 7 AND 200 MM SODIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.19→34.27 Å / Num. obs: 34091 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.5
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KAW

3kaw


Resolution: 1.194→52.75 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.3 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 14-16 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1721 5.14 %RANDOM
Rwork0.1365 ---
obs0.138 34049 98.291 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.938 Å2
Baniso -1Baniso -2Baniso -3
1-0.131 Å20 Å20 Å2
2---0.062 Å20 Å2
3----0.068 Å2
Refinement stepCycle: LAST / Resolution: 1.194→52.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 0 82 1024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019976
X-RAY DIFFRACTIONr_bond_other_d0.0020.02917
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.9461314
X-RAY DIFFRACTIONr_angle_other_deg1.10832125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0945134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.35423.86444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54915184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7881510
X-RAY DIFFRACTIONr_chiral_restr0.1140.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021123
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02211
X-RAY DIFFRACTIONr_nbd_refined0.2690.2592
X-RAY DIFFRACTIONr_nbd_other0.1840.284
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2982
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0680.210
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.22
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_it2.0421.316516
X-RAY DIFFRACTIONr_mcbond_other1.7311.309515
X-RAY DIFFRACTIONr_mcangle_it2.1221.97643
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9021.716460
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4762.45666
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.42631893
X-RAY DIFFRACTIONr_sphericity_free20.388526
X-RAY DIFFRACTIONr_sphericity_bonded10.4291938
LS refinement shellResolution: 1.194→1.225 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 111 -
Rwork0.222 2381 -
obs--98.771 %

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