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- PDB-4nyo: The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Ca... -

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Basic information

Entry
Database: PDB / ID: 4nyo
TitleThe 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta from Pyrococcus Horikoshii OT3
ComponentsDivalent-cation tolerance protein CutA
KeywordsMETAL BINDING PROTEIN / Copper Tolerance / Cuta / Structural Genomics / Riken Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


response to metal ion / metal 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
Divalent-cation tolerance protein CutA
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBagautdinov, B. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: ACTA CRYSTALLOGR.,SECT.F / Year: 2014
Title: The structures of the CutA1 proteins from Thermus thermophilus and Pyrococcus horikoshii: characterization of metal-binding sites and metal-induced assembly
Authors: Bagautdinov, B.
History
DepositionDec 11, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 1, 2014ID: 4LU7
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Other
Revision 1.3Nov 8, 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_sheet / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_sheet.number_strands / _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: Divalent-cation tolerance protein CutA
B: Divalent-cation tolerance protein CutA
C: Divalent-cation tolerance protein CutA
D: Divalent-cation tolerance protein CutA
E: Divalent-cation tolerance protein CutA
F: Divalent-cation tolerance protein CutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,69822
Polymers74,3956
Non-polymers1,30316
Water12,394688
1
A: Divalent-cation tolerance protein CutA
B: Divalent-cation tolerance protein CutA
C: Divalent-cation tolerance protein CutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,84911
Polymers37,1983
Non-polymers6518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-102 kcal/mol
Surface area13020 Å2
MethodPISA
2
D: Divalent-cation tolerance protein CutA
E: Divalent-cation tolerance protein CutA
F: Divalent-cation tolerance protein CutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,84911
Polymers37,1983
Non-polymers6518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-117 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.085, 124.250, 50.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Divalent-cation tolerance protein CutA


Mass: 12399.188 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: cutA, PH0992 / Plasmid: PET-11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O58720

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Non-polymers , 5 types, 704 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 1.96 Å3/Da / Density % sol: 37.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: PEG 4000, MES, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 16, 2003 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→36.1 Å / Num. obs: 53038 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.12 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.7
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 4.1 / % possible all: 86.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NZA

1nza


Resolution: 1.8→36.1 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2691 -RANDOM
Rwork0.189 ---
obs0.189 53038 96.3 %-
Displacement parametersBiso mean: 26.67 Å2
Baniso -1Baniso -2Baniso -3
1-11.25 Å20 Å20 Å2
2---6.81 Å20 Å2
3----4.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 68 688 6006
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 312 -
Rwork0.291 --
obs--86.2 %

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