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- PDB-4e98: Crystal structure of possible CutA1 divalent ion tolerance protei... -

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Basic information

Entry
Database: PDB / ID: 4.0E+98
TitleCrystal structure of possible CutA1 divalent ion tolerance protein from Cryptosporidium parvum Iowa II
ComponentsCutA1 divalent ion tolerance protein
KeywordsSIGNALING PROTEIN / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


response to metal ion / copper ion binding
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 homolog
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Buchko, G.W. / Robinson, H.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structure of a CutA1 divalent-cation tolerance protein from Cryptosporidium parvum, the protozoal parasite responsible for cryptosporidiosis.
Authors: Buchko, G.W. / Abendroth, J. / Clifton, M.C. / Robinson, H. / Zhang, Y. / Hewitt, S.N. / Staker, B.L. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Jun 3, 2015Group: Database references
Revision 1.4Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: CutA1 divalent ion tolerance protein
B: CutA1 divalent ion tolerance protein
C: CutA1 divalent ion tolerance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8636
Polymers46,7573
Non-polymers1063
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-68 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.460, 55.590, 67.290
Angle α, β, γ (deg.)90.00, 108.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CutA1 divalent ion tolerance protein


Mass: 15585.688 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd6_2410 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5CX58
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1.79 Å3/Da / Density % sol: 31.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Emerald Bio Precipitant Synergy Screen: 30% PEG1500, 20% PEG400, 100 mM HEPES, pH 7.5, CRPAA.01087.AA1 PB00061 at 3 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 22608 / Num. obs: 22553 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.58 / Num. unique all: 1661 / Rsym value: 0.472 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NZA

1nza


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.76 / SU ML: 0.124 / Isotropic thermal model: ISOTROPIC, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1153 5.1 %RANDOM
Rwork0.198 ---
all0.2 22608 --
obs0.2 22552 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.04 Å2
2---0.71 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 3 191 2734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022602
X-RAY DIFFRACTIONr_bond_other_d0.0060.021667
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9623549
X-RAY DIFFRACTIONr_angle_other_deg1.43234152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93226.075107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87715480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.489156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022809
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02457
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 75 -
Rwork0.23 1521 -
obs-1660 100 %
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)
10.69520.24140.02371.3489-0.2620.54040.0250.0496-0.04560.0839-0.0368-0.07370.01510.10540.01190.07710.0091-0.04950.0243-0.00790.071635.7059.1115.227
21.1806-0.181-0.07340.93240.47760.3939-0.04810.0191-0.07260.090.01660.09260.0879-0.04230.03140.1019-0.0016-0.03420.02020.00470.100117.1354.64516.041
31.4237-0.03230.18060.7129-0.10110.485-0.0115-0.01340.1370.0046-0.01120.0332-0.1026-0.02710.02270.07250.0048-0.02640.0046-0.00010.079123.78522.6416.663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 115
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1A301 - 303
4X-RAY DIFFRACTION2B10 - 115
5X-RAY DIFFRACTION2B201
6X-RAY DIFFRACTION2B301 - 303
7X-RAY DIFFRACTION3C12 - 116
8X-RAY DIFFRACTION3C201
9X-RAY DIFFRACTION3C301 - 303

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