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- PDB-5fjd: APO-CSP1 (COPPER STORAGE PROTEIN 1) FROM METHYLOSINUS TRICHOSPORI... -

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Basic information

Entry
Database: PDB / ID: 5fjd
TitleAPO-CSP1 (COPPER STORAGE PROTEIN 1) FROM METHYLOSINUS TRICHOSPORIUM OB3B
ComponentsCOPPER STORAGE PROTEIN 1
KeywordsCOPPER BINDING PROTEIN / METHANE OXIDATION / COPPER STORAGE / METHANOTROPHS / PARTICULATE METHANE MONOOXYGENASE
Function / homologyTwin-arginine translocation signal, Cys-rich four helix bundle protein / metal ion binding / Copper storage protein 1
Function and homology information
Biological speciesMETHYLOSINUS TRICHOSPORIUM OB3B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVita, N. / Platsaki, S. / Basle, A. / Allen, S.J. / Paterson, N.G. / Crombie, A.T. / Murrell, J.C. / Waldron, K.J. / Dennison, C.
CitationJournal: Nature / Year: 2015
Title: A Four-Helix Bundle Stores Copper for Methane Oxidation.
Authors: Vita, N. / Platsaki, S. / Basle, A. / Allen, S.J. / Paterson, N.G. / Waldron, K.J. / Dennison, C.
History
DepositionOct 7, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionNov 18, 2015ID: 5AJE
Revision 1.0Nov 18, 2015Provider: 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: COPPER STORAGE PROTEIN 1
B: COPPER STORAGE PROTEIN 1
C: COPPER STORAGE PROTEIN 1
D: COPPER STORAGE PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)50,4384
Polymers50,4384
Non-polymers00
Water7,314406
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-68.7 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.885, 105.918, 48.657
Angle α, β, γ (deg.)90.00, 112.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
COPPER STORAGE PROTEIN 1


Mass: 12609.529 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHYLOSINUS TRICHOSPORIUM OB3B (bacteria)
Plasmid: PET29A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL60*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 1.93 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS, PH 6.5, 25% W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→44.95 Å / Num. obs: 60896 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AJF

5ajf
PDB Unreleased entry


Resolution: 1.5→52.96 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.152 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17913 3089 5.1 %RANDOM
Rwork0.12249 ---
obs0.12535 57772 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.052 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.99 Å2
2---0.6 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→52.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 0 406 3546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193268
X-RAY DIFFRACTIONr_bond_other_d0.0150.023175
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.9514416
X-RAY DIFFRACTIONr_angle_other_deg2.1263.0147231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0345461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.12225.351114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11815548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.673155
X-RAY DIFFRACTIONr_chiral_restr0.1070.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023781
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02680
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_it2.1161.3291791
X-RAY DIFFRACTIONr_mcbond_other2.1111.3281790
X-RAY DIFFRACTIONr_mcangle_it2.4272.0032239
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1181.811477
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_restr5.3436443
X-RAY DIFFRACTIONr_sphericity_free36.101580
X-RAY DIFFRACTIONr_sphericity_bonded13.96356710
LS refinement shellResolution: 1.5→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 245 -
Rwork0.182 4233 -
obs--99.73 %

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