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- PDB-1p1l: Structure of the Periplasmic divalent cation tolerance protein Cu... -

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Basic information

Entry
Database: PDB / ID: 1p1l
TitleStructure of the Periplasmic divalent cation tolerance protein CutA from Archaeoglobus fulgidus
ComponentsPeriplasmic divalent cation tolerance protein CUTA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / T835 / NYSGXRC / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
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
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2 Å
AuthorsKniewel, R. / Buglino, J.A. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published / Year: 2003
Title: Structure of the Periplasmic divalent cation tolerance protein CutA from Archaeoglobus fulgidus
Authors: Kniewel, R. / Buglino, J.A. / Lima, C.D.
History
DepositionApr 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic divalent cation tolerance protein CUTA


Theoretical massNumber of molelcules
Total (without water)11,9011
Polymers11,9011
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Periplasmic divalent cation tolerance protein CUTA

A: Periplasmic divalent cation tolerance protein CUTA

A: Periplasmic divalent cation tolerance protein CUTA


Theoretical massNumber of molelcules
Total (without water)35,7033
Polymers35,7033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6870 Å2
ΔGint-59 kcal/mol
Surface area12610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.967, 90.967, 90.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Cell settingcubic
Space group name H-MI213

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Components

#1: Protein Periplasmic divalent cation tolerance protein CUTA / cutA


Mass: 11900.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: CUTA / Production host: Escherichia coli (E. coli) / References: UniProt: O28301
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 21% PEG 1500, 0.1M Na Citrate pH 5.6, 3% MPD, 0.15M Magnesium Chloride, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
1,21
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEMar 12, 2003osmic multilayer
RIGAKU RAXIS IV2IMAGE PLATEMar 13, 2003osmic multilayer
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1OSMICSINGLE WAVELENGTHMx-ray1
2OSMICSIRMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 8551 / Num. obs: 8551 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 37.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 11 / % possible all: 79.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS0.9refinement
RESOLVEphasing
RefinementMethod to determine structure: SIR / Resolution: 2→19.4 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 438 5.1 %RANDOM
Rwork0.207 ---
all0.2071 8534 --
obs0.2071 8534 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6094 Å2 / ksol: 0.398561 e/Å3
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms836 0 0 56 892
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it0.911.5
X-RAY DIFFRACTIONc_mcangle_it1.432
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.214 47 5.7 %
Rwork0.195 774 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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