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- PDB-5fig: APO-CSP3 (COPPER STORAGE PROTEIN 3) FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 5fig
TitleAPO-CSP3 (COPPER STORAGE PROTEIN 3) FROM BACILLUS SUBTILIS
ComponentsCSP3
KeywordsCOPPER-BINDING PROTEIN / COPPER STORAGE / BACILLUS SUBTILIS
Function / homologySubstrate Binding Domain Of Dnak; Chain:A; Domain 2 - #360 / Protein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha / Uncharacterized cysteine-rich protein YhjQ
Function and homology information
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVita, N. / Landolfi, G. / Basle, A. / Platsaki, S. / Waldron, K. / Dennison, C.
CitationJournal: Sci Rep / Year: 2016
Title: Bacterial cytosolic proteins with a high capacity for Cu(I) that protect against copper toxicity.
Authors: Vita, N. / Landolfi, G. / Basle, A. / Platsaki, S. / Lee, J. / Waldron, K.J. / Dennison, C.
History
DepositionSep 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_beamline
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 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
B: CSP3
C: CSP3
D: CSP3
E: CSP3
F: CSP3


Theoretical massNumber of molelcules
Total (without water)71,1236
Polymers71,1236
Non-polymers00
Water2,468137
1
A: CSP3
B: CSP3
C: CSP3
D: CSP3


Theoretical massNumber of molelcules
Total (without water)47,4154
Polymers47,4154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-28.7 kcal/mol
Surface area14960 Å2
MethodPISA
2
E: CSP3
F: CSP3

E: CSP3
F: CSP3


Theoretical massNumber of molelcules
Total (without water)47,4154
Polymers47,4154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area7060 Å2
ΔGint-25.8 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.087, 126.510, 85.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-2012-

HOH

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Components

#1: Protein
CSP3


Mass: 11853.758 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) BACILLUS SUBTILIS (bacteria) / References: UniProt: O07571*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growDetails: 200 MM NACL, 100 MM CITRATE PH 4, 800 MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Type: DIAMOND / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→45.41 Å / Num. obs: 64008 / % possible obs: 98.7 % / Observed criterion σ(I): 1.5 / Redundancy: 5.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.5 / % possible all: 98

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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: 1.7→81.74 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.128 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24262 3180 5 %RANDOM
Rwork0.21971 ---
obs0.22085 60813 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.231 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.59 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→81.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 0 137 4457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194466
X-RAY DIFFRACTIONr_bond_other_d0.0140.024101
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.9536003
X-RAY DIFFRACTIONr_angle_other_deg2.3853.0029561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1645608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.38825.249181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93215825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1321519
X-RAY DIFFRACTIONr_chiral_restr0.1020.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025082
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02921
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_it0.5320.7842372
X-RAY DIFFRACTIONr_mcbond_other0.530.7832371
X-RAY DIFFRACTIONr_mcangle_it0.911.1652949
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0130.9452094
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 225 -
Rwork0.279 4444 -
obs--99.34 %
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)
12.4505-0.22020.33732.6907-0.15492.4436-0.078-0.1050.1079-0.07430.06610.1213-0.0042-0.22920.01190.0519-0.0763-0.01220.15310.00580.011716.72829.408945.7641
22.7964-0.4259-0.21462.57120.29932.6923-0.0944-0.0451-0.1779-0.09780.1226-0.0899-0.01480.2593-0.02820.0588-0.08520.01430.1569-0.00990.017337.725634.131145.0484
33.45810.17860.27172.4696-0.40292.90030.0508-0.1838-0.24460.1056-0.059-0.14270.26920.11740.00820.1549-0.0720.00490.13750.01780.031227.664820.258963.314
43.04130.4595-0.60732.66230.3783.31010.0386-0.16210.13560.0796-0.04030.1525-0.2444-0.15960.00180.1463-0.0682-0.00330.1292-0.0120.014928.738141.22964.0838
54.08010.02780.60731.74720.0053.0833-0.11650.1352-0.0926-0.11330.0971-0.109-0.11940.0560.01940.0973-0.06770.02380.0762-0.01430.01297.88948.272833.6669
63.6596-0.40560.52331.6276-0.15583.4973-0.1136-0.09740.120.08850.05310.0881-0.26230.06140.06050.09190.03340.00560.05320.00390.0121-7.16938.304351.8645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 108
2X-RAY DIFFRACTION2B2 - 108
3X-RAY DIFFRACTION3C4 - 108
4X-RAY DIFFRACTION4D4 - 108
5X-RAY DIFFRACTION5E4 - 108
6X-RAY DIFFRACTION6F4 - 108

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