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- PDB-1uku: Crystal Structure of Pyrococcus horikoshii CutA1 Complexed with Cu2+ -

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Basic information

Entry
Database: PDB / ID: 1uku
TitleCrystal Structure of Pyrococcus horikoshii CutA1 Complexed with Cu2+
Componentsperiplasmic divalent cation tolerance protein CutA
KeywordsMETAL BINDING PROTEIN / CUTA / COPPER TOLERANCE / structural genomics
Function / homology
Function and homology information


response to metal ion / copper ion binding / cytoplasm
Similarity search - Function
Divalent ion tolerance protein, CutA / CutA1 divalent ion tolerance protein / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Divalent-cation tolerance protein CutA
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTanaka, Y. / Yasutake, Y. / Yao, M. / Sakai, N. / Tanaka, I. / Tsumoto, K. / Kumagai, I.
CitationJournal: Febs Lett. / Year: 2004
Title: Structural implications for heavy metal-induced reversible assembly and aggregation of a protein: the case of Pyrococcus horikoshii CutA.
Authors: Tanaka, Y. / Tsumoto, K. / Nakanishi, T. / Yasutake, Y. / Sakai, N. / Yao, M. / Tanaka, I. / Kumagai, I.
History
DepositionSep 1, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_special_symmetry / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: periplasmic divalent cation tolerance protein CutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4312
Polymers12,3671
Non-polymers641
Water1,26170
1
A: periplasmic divalent cation tolerance protein CutA
hetero molecules

A: periplasmic divalent cation tolerance protein CutA
hetero molecules

A: periplasmic divalent cation tolerance protein CutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2926
Polymers37,1023
Non-polymers1913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6330 Å2
ΔGint-47 kcal/mol
Surface area12950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.242, 52.242, 54.111
Angle α, β, γ (deg.)90, 90, 120
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-150-

CU

21A-266-

HOH

31A-267-

HOH

41A-268-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: (-y+1, x-y, z) and (y-x+1, -x+1, z).

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Components

#1: Protein periplasmic divalent cation tolerance protein CutA / CutA1


Mass: 12367.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0992 / Plasmid: pET20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58720
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.73 Å3/Da / Density % sol: 28.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 100mM acetate buffer, 1.5M ammonium sulfate, 2mM CuSO4, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2003
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. all: 15562 / Num. obs: 15562 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 11.781 Å2 / Rsym value: 0.052 / Net I/σ(I): 9.3
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 7.2 % / Num. unique all: 1532 / Rsym value: 0.36 / % possible all: 99.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1j2v

1j2v


Resolution: 1.45→10 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.142 / SU ML: 0.045 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.075 / ESU R Free: 0.076 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19415 1555 10.1 %RANDOM
Rwork0.16168 ---
all0.165 13822 --
obs0.16488 13822 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 10.696 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 1 70 944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021893
X-RAY DIFFRACTIONr_bond_other_d0.0020.02822
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9531208
X-RAY DIFFRACTIONr_angle_other_deg0.79731916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965101
X-RAY DIFFRACTIONr_chiral_restr0.0870.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02956
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02177
X-RAY DIFFRACTIONr_nbd_refined0.2080.2145
X-RAY DIFFRACTIONr_nbd_other0.260.2848
X-RAY DIFFRACTIONr_nbtor_other0.0810.2521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3540.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3760.215
X-RAY DIFFRACTIONr_mcbond_it0.8741.5511
X-RAY DIFFRACTIONr_mcangle_it1.6492833
X-RAY DIFFRACTIONr_scbond_it2.5313382
X-RAY DIFFRACTIONr_scangle_it3.9814.5375
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.208 117
Rwork0.19 969

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