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- PDB-1naq: Crystal structure of CUTA1 from E.coli at 1.7 A resolution -

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Basic information

Entry
Database: PDB / ID: 1naq
TitleCrystal structure of CUTA1 from E.coli at 1.7 A resolution
ComponentsPeriplasmic divalent cation tolerance protein cutA
KeywordsELECTRON TRANSPORT / CUTA / copper resistance / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


response to copper ion / copper ion binding / protein-containing complex / metal ion binding / cytoplasm
Similarity search - Function
Divalent cation tolerance protein CutA, Enterobacteria / 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
: / MERCURIBENZOIC ACID / Divalent-cation tolerance protein CutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsCalderone, V. / Mangani, S. / Benvenuti, M. / Viezzoli, M.S. / Banci, L. / Bertini, I. / Structural Proteomics in Europe (SPINE)
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: The evolutionarily conserved trimeric structure of CutA1 proteins suggests a role in signal transduction.
Authors: Arnesano, F. / Banci, L. / Benvenuti, M. / Bertini, I. / Calderone, V. / Mangani, S. / Viezzoli, M.S.
#1: Journal: To be Published
Title: STRUCTURE OF PROTEIN TM1056, CUTA
Authors: SAVCHENKO, A. / ZHANG, R. / JOACHIMIAK, A. / EDWARDS, A. / AKARINA, T.
History
DepositionNov 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Remark 600HETEROGEN P-HYDROXYMERCURIBENZOIC ACID HAS BEEN ADDED TO THE PROTEIN PRIOR TO CRYSTALLISATION. IT ...HETEROGEN P-HYDROXYMERCURIBENZOIC ACID HAS BEEN ADDED TO THE PROTEIN PRIOR TO CRYSTALLISATION. IT REACTS WITH THE -SH OF FREE CYSTEINS AND, BY THE ELIMINATION OF ONE WATER MOLECULE, FORMS A COVALENT BOND BETWEEN THE S OF THE CYS AND HG WHICH IS THEN A GOOD CANDIDATE TO PERFORM A MAD EXPERIMENT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic divalent cation tolerance protein cutA
B: Periplasmic divalent cation tolerance protein cutA
C: Periplasmic divalent cation tolerance protein cutA
D: Periplasmic divalent cation tolerance protein cutA
E: Periplasmic divalent cation tolerance protein cutA
F: Periplasmic divalent cation tolerance protein cutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,87424
Polymers74,0526
Non-polymers4,82218
Water6,179343
1
A: Periplasmic divalent cation tolerance protein cutA
B: Periplasmic divalent cation tolerance protein cutA
C: Periplasmic divalent cation tolerance protein cutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,43712
Polymers37,0263
Non-polymers2,4119
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-170 kcal/mol
Surface area13340 Å2
MethodPISA
2
D: Periplasmic divalent cation tolerance protein cutA
E: Periplasmic divalent cation tolerance protein cutA
F: Periplasmic divalent cation tolerance protein cutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,43712
Polymers37,0263
Non-polymers2,4119
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-168 kcal/mol
Surface area13310 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21470 Å2
ΔGint-350 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.989, 89.563, 122.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological functional unit is a trimer; the asymmetric unit is made of two trimers.

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Components

#1: Protein
Periplasmic divalent cation tolerance protein cutA / C-type cytochrome biogenesis protein cycY


Mass: 12342.025 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CUTA / Production host: Escherichia coli (E. coli) / References: UniProt: P69488
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C7H5HgO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Na HEPES, 2M Ammonium sulphate, 2% PEG 400, 2 mM 4-(hydroxymercuri)benzoic acid, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.5
32.0 Mammonium sulfate1reservoir
42 %PEG4001reservoir
53 mM4-(hydroxymercuri)benzoic acid1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.005231, 1.00870, 0.93200
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 14, 2002
RadiationMonochromator: Double crystal focussing monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0052311
21.00871
30.9321
ReflectionResolution: 1.7→37.5 Å / Num. all: 65739 / Num. obs: 65739 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 18.95 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.1 / Num. unique all: 9337 / Rsym value: 0.619 / % possible all: 96.3
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 643844
Reflection shell
*PLUS
% possible obs: 96.3 % / Num. unique obs: 9337 / Num. measured obs: 90452 / Rmerge(I) obs: 0.519

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.80refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 3.338 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.164 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: At the N-terminus of all the six molecules present in the asymetric unit there are about 6-8 residues for which it's not possible to see a clear density. Among the densities belonging to ...Details: At the N-terminus of all the six molecules present in the asymetric unit there are about 6-8 residues for which it's not possible to see a clear density. Among the densities belonging to each asymmetric unit it's possible to see some extra density which could account for the presence of some crystalline PEG fragments.
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 5522 8.4 %RANDOM
Rwork0.2025 ---
all0.20702 ---
obs0.20702 50036 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.738 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati sigma a obs: 0.055714 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 113 343 5287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215023
X-RAY DIFFRACTIONr_angle_refined_deg1.9941.9826871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.225622
X-RAY DIFFRACTIONr_chiral_restr0.1550.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023713
X-RAY DIFFRACTIONr_nbd_refined0.3110.21813
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.40.279
X-RAY DIFFRACTIONr_mcbond_it1.1591.53146
X-RAY DIFFRACTIONr_mcangle_it1.93425084
X-RAY DIFFRACTIONr_scbond_it3.11231877
X-RAY DIFFRACTIONr_scangle_it4.6864.51787
LS refinement shellResolution: 1.7→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 784 -
Rwork0.252 4348 -
obs-9337 96.3 %
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.99

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