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- PDB-1aqp: RIBONUCLEASE A COPPER COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1aqp
TitleRIBONUCLEASE A COPPER COMPLEX
DescriptorRIBONUCLEASE A
KeywordsHYDROLASE (PHOSPHORIC DIESTER)
Specimen sourceBos taurus / mammal / cattle / ウシ /
MethodX-ray diffraction (2 Å resolution / Molecular replacement)
AuthorsRamasubbu, N.
CitationProc.Natl.Acad.Sci.USA, 1997, 94, 9620-9625

Proc.Natl.Acad.Sci.USA, 1997, 94, 9620-9625 Yorodumi Papers
Crystal structures of the copper and nickel complexes of RNase A: metal-induced interprotein interactions and identification of a novel copper binding motif.
Balakrishnan, R. / Ramasubbu, N. / Varughese, K.I. / Parthasarathy, R.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 31, 1997 / Release: May 27, 1998
RevisionDateData content typeGroupProviderType
1.0May 27, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8353
Polyers13,7081
Non-polymers1272
Water1,49583
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)58.180, 53.800, 42.900
Angle α, β, γ (deg.)90.00, 118.90, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

#1: Polypeptide(L)RIBONUCLEASE A / RNASE A


Mass: 13708.326 Da / Num. of mol.: 1 / Details: COPPER COMPLEX / Source: (natural) Bos taurus / mammal / ウシ / / References: UniProt: P61823, EC: 3.1.27.5

Cellular component

Molecular function

#2: ChemicalChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Formula: Cu
#3: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.18 / Density percent sol: 45
Crystal growpH: 5.5
Details: ENZYME WAS CRYSTALLIZED FROM MPD WITH 6 MOLAR EXCESS OF COPPER, pH 5.5
Crystal grow
*PLUS
Temp unit: K / Method: unknown

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Data collection

DiffractionMean temperature: 287 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Details: COLLIMATOR / Detector: IMAGE PLATE / Collection date: Oct 1, 1996
RadiationMonochromator: NI / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2 Å / D resolution low: 5 Å / Number obs: 6930 / Observed criterion sigma I: 2 / Rmerge I obs: 0.038 / Rsym value: 0.041 / NetI over sigmaI: 13 / Redundancy: 2.5 / Percent possible obs: 85
Reflection shellRmerge I obs: 0.08 / Highest resolution: 2 Å / Lowest resolution: 2.11 Å / MeanI over sigI obs: 9 / Rsym value: 0.08 / Redundancy: 1.5 / Percent possible all: 55
Reflection shell
*PLUS
Percent possible obs: 55

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7RSA
Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Sigma F: 2
Displacement parametersB iso mean: 18.5 Å2
Least-squares processR factor R work: 0.2 / R factor obs: 0.2 / Highest resolution: 2 Å / Lowest resolution: 8 Å / Number reflection obs: 6610 / Percent reflection obs: 85
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 4 Å
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 1196 / Nucleic acid: 0 / Ligand: 2 / Solvent: 82 / Total: 1280
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.0
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.0
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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