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- PDB-3k7r: Crystal structure of [TM][CuAtx1]3 -

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Basic information

Entry
Database: PDB / ID: 3k7r
TitleCrystal structure of [TM][CuAtx1]3
ComponentsMetal homeostasis factor ATX1
KeywordsCHAPERONE / ferredoxin-like fold / protein-metal-drug complex / Cu-Mo metal cluster / Copper transport / Ion transport / Metal-binding / Transport
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
TETRATHIOMOLYBDATE / COPPER (II) ION / D-MALATE / Copper chaperone ATX1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular replacement, MAD / Resolution: 2.28 Å
AuthorsXue, Y. / Alvarez, H.M. / Robinson, C.D. / Mondragon, A. / O'Halloran, T.V.
CitationJournal: Science / Year: 2010
Title: Tetrathiomolybdate inhibits copper trafficking proteins through metal cluster formation.
Authors: Alvarez, H.M. / Xue, Y. / Robinson, C.D. / Canalizo-Hernandez, M.A. / Marvin, R.G. / Kelly, R.A. / Mondragon, A. / Penner-Hahn, J.E. / O'Halloran, T.V.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 6, 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 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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 / _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: 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
I: Metal homeostasis factor ATX1
J: Metal homeostasis factor ATX1
K: Metal homeostasis factor ATX1
L: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,97434
Polymers98,79212
Non-polymers2,18222
Water6,539363
1
A: Metal homeostasis factor ATX1
B: Metal homeostasis factor ATX1
C: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1768
Polymers24,6983
Non-polymers4785
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Metal homeostasis factor ATX1
E: Metal homeostasis factor ATX1
F: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3109
Polymers24,6983
Non-polymers6126
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Metal homeostasis factor ATX1
H: Metal homeostasis factor ATX1
I: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1768
Polymers24,6983
Non-polymers4785
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Metal homeostasis factor ATX1
K: Metal homeostasis factor ATX1
L: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3109
Polymers24,6983
Non-polymers6126
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,48717
Polymers49,3966
Non-polymers1,09111
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-113 kcal/mol
Surface area22110 Å2
MethodPISA
6
G: Metal homeostasis factor ATX1
H: Metal homeostasis factor ATX1
I: Metal homeostasis factor ATX1
J: Metal homeostasis factor ATX1
K: Metal homeostasis factor ATX1
L: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,48717
Polymers49,3966
Non-polymers1,09111
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-112 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.887, 182.242, 52.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

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Components

#1: Protein
Metal homeostasis factor ATX1


Mass: 8232.650 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATX1, N0840, YNL259C / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38636
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-4SM / TETRATHIOMOLYBDATE


Mass: 224.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: MoS4
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 7
Details: 0.15 M DL-Malic acid, pH 7.0, 20% PEG 3350, EVAPORATION, temperature 287K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11.3799, 1.3805, 1.3850
SYNCHROTRONAPS 19-BM20.9787
DetectorType: ADSC QUANTUM 210 / Detector: CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.37991
21.38051
31.3851
40.97871
ReflectionResolution: 2.28→50 Å / Num. obs: 47445 / % possible obs: 97 % / Redundancy: 5 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.7
Reflection shellResolution: 2.28→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / Num. unique all: 3998 / % possible all: 84

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
SHARPphasing
autoSHARPphasing
REFMAC5.5.0102refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: Molecular replacement, MAD
Starting model: PDB ENTRY 1CC8

1cc8


Resolution: 2.28→37.42 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.557 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25612 2404 5.1 %RANDOM
Rwork0.20174 ---
obs0.2045 44981 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.464 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.28→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6740 0 54 363 7157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226932
X-RAY DIFFRACTIONr_angle_refined_deg1.7582.0039232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755845
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.14726.175251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.473151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.5791512
X-RAY DIFFRACTIONr_chiral_restr0.1160.21111
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214784
X-RAY DIFFRACTIONr_mcbond_it0.7281.54253
X-RAY DIFFRACTIONr_mcangle_it1.33526956
X-RAY DIFFRACTIONr_scbond_it2.48632679
X-RAY DIFFRACTIONr_scangle_it3.9764.52275
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 516 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.470.5
Bmedium positional0.440.5
Cmedium positional0.590.5
Dmedium positional0.420.5
Emedium positional0.480.5
Fmedium positional0.40.5
Gmedium positional0.550.5
Hmedium positional0.50.5
Imedium positional0.450.5
Jmedium positional0.550.5
Kmedium positional0.430.5
Lmedium positional0.590.5
Amedium thermal1.362
Bmedium thermal1.142
Cmedium thermal1.672
Dmedium thermal1.422
Emedium thermal1.252
Fmedium thermal1.692
Gmedium thermal1.552
Hmedium thermal1.172
Imedium thermal1.232
Jmedium thermal2.162
Kmedium thermal1.212
Lmedium thermal1.832
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 133 -
Rwork0.269 2471 -
obs--72.51 %
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)
10.6740.1624-0.63151.6144-1.07923.55320.0069-0.08980.15440.21230.02210.1461-0.1137-0.3136-0.02890.10130.01490.0040.0769-0.06910.097816.908138.761821.7768
21.84520.1439-1.07180.8561-0.14981.01910.01740.3428-0.003-0.0297-0.0666-0.0186-0.0291-0.30820.04920.0522-0.0016-0.02980.1113-0.02820.056615.044418.651414.9694
31.36591.26331.11051.9810.5871.8229-0.2103-0.08610.32890.0719-0.04760.2742-0.4599-0.11670.25790.13970.0218-0.03230.0384-0.01040.20169.391520.065529.6004
40.5493-0.4623-0.33080.9248-0.13670.5926-0.0407-0.0334-0.04750.2218-0.0294-0.0166-0.10630.00340.07020.072-0.0333-0.01670.048-0.02110.090381.656310.926345.0874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 72
2X-RAY DIFFRACTION1B2 - 73
3X-RAY DIFFRACTION1C2 - 73
4X-RAY DIFFRACTION2D2 - 73
5X-RAY DIFFRACTION2E2 - 73
6X-RAY DIFFRACTION2F2 - 73
7X-RAY DIFFRACTION3G2 - 73
8X-RAY DIFFRACTION3H4 - 73
9X-RAY DIFFRACTION3I3 - 73
10X-RAY DIFFRACTION4J2 - 73
11X-RAY DIFFRACTION4K2 - 73
12X-RAY DIFFRACTION4L2 - 69

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