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- PDB-5vdf: Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II -

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Basic information

Entry
Database: PDB / ID: 5vdf
TitleCrystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II
ComponentsMetal homeostasis factor ATX1
KeywordsMETAL BINDING PROTEIN / Atx1 / metallochaperone / copper transfer / metal-binding domain / ferredoxin-like fold
Function / homology
Function and homology information


copper chaperone activity / copper ion transport / cellular response to oxidative stress / intracellular iron ion homeostasis / metal ion binding / cytosol
Similarity search - Function
Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (I) ION / Copper chaperone ATX1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLee, M. / Maher, M.J.
CitationJournal: J. Inorg. Biochem. / Year: 2017
Title: The crystal structures of a copper-bound metallochaperone from Saccharomyces cerevisiae.
Authors: Lee, M. / Cooray, N.D.G. / Maher, M.J.
History
DepositionApr 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal homeostasis factor ATX1
B: Metal homeostasis factor ATX1
C: Metal homeostasis factor ATX1
D: Metal homeostasis factor ATX1
E: Metal homeostasis factor ATX1
F: Metal homeostasis factor ATX1
G: Metal homeostasis factor ATX1
H: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,11512
Polymers65,8618
Non-polymers2544
Water3,135174
1
A: Metal homeostasis factor ATX1
B: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Metal homeostasis factor ATX1
D: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Metal homeostasis factor ATX1
F: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Metal homeostasis factor ATX1
H: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Metal homeostasis factor ATX1
hetero molecules

B: Metal homeostasis factor ATX1


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1050 Å2
ΔGint-7 kcal/mol
Surface area7950 Å2
MethodPISA
6
C: Metal homeostasis factor ATX1
hetero molecules

D: Metal homeostasis factor ATX1


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1010 Å2
ΔGint-7 kcal/mol
Surface area7930 Å2
MethodPISA
7
G: Metal homeostasis factor ATX1
H: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-7 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.148, 114.385, 58.135
Angle α, β, γ (deg.)90.00, 92.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Metal homeostasis factor ATX1


Mass: 8232.650 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ATX1, YNL259C, N0840 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38636
#2: Chemical
ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 0.1 M HEPES (pH 7.9), 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.93→58.09 Å / Num. obs: 45429 / % possible obs: 99.5 % / Redundancy: 4.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.075 / Net I/σ(I): 9.8
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2967 / CC1/2: 0.662 / Rpim(I) all: 0.669 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CC8

1cc8


Resolution: 1.93→58.09 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.648 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24175 2301 5.1 %RANDOM
Rwork0.19542 ---
obs0.19782 42701 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.254 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.41 Å2
2---1.21 Å20 Å2
3---1.77 Å2
Refinement stepCycle: 1 / Resolution: 1.93→58.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 4 174 4626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194509
X-RAY DIFFRACTIONr_bond_other_d0.0020.024507
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9926055
X-RAY DIFFRACTIONr_angle_other_deg0.876310526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.44326.098164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69815931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.123158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024741
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02767
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_it1.8522.8922253
X-RAY DIFFRACTIONr_mcbond_other1.8512.8912252
X-RAY DIFFRACTIONr_mcangle_it2.9394.3092798
X-RAY DIFFRACTIONr_mcangle_other2.944.312799
X-RAY DIFFRACTIONr_scbond_it2.4113.2992256
X-RAY DIFFRACTIONr_scbond_other2.4113.2992256
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9624.7943255
X-RAY DIFFRACTIONr_long_range_B_refined5.82434.0514834
X-RAY DIFFRACTIONr_long_range_B_other5.77433.9344808
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 158 -
Rwork0.309 2967 -
obs--94.58 %

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