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- PDB-1x1u: Water-mediate interaction at aprotein-protein interface -

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Basic information

Entry
Database: PDB / ID: 1x1u
TitleWater-mediate interaction at aprotein-protein interface
Components
  • Barstar
  • Ribonuclease
KeywordsHydrolase/Protein Binding / Rnase-inhibitor complex / Hydrolase/Hydrolase inhibitor / Hydrolase-Protein Binding COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region / cytoplasm
Similarity search - Function
Barstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / : / Barnase / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin ...Barstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / : / Barnase / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease / Barstar
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIkura, T. / Urakubo, Y. / Ito, N.
CitationJournal: Chem.Phys. / Year: 2004
Title: Water-mediated interaction at a protein-protein interface
Authors: Ikura, T. / Urakubo, Y. / Ito, N.
History
DepositionApr 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease
B: Ribonuclease
C: Ribonuclease
D: Barstar
E: Barstar
F: Barstar


Theoretical massNumber of molelcules
Total (without water)67,6686
Polymers67,6686
Non-polymers00
Water8,971498
1
A: Ribonuclease
D: Barstar


Theoretical massNumber of molelcules
Total (without water)22,5562
Polymers22,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease
E: Barstar


Theoretical massNumber of molelcules
Total (without water)22,5562
Polymers22,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease
F: Barstar


Theoretical massNumber of molelcules
Total (without water)22,5562
Polymers22,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.278, 43.805, 83.310
Angle α, β, γ (deg.)90.00, 110.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-173-

HOH

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Components

#1: Protein Ribonuclease / Barnase / RNase Ba


Mass: 12398.721 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: PML2BS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)[PLYSE]
References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Protein Barstar / Ribonuclease inhibitor


Mass: 10157.412 Da / Num. of mol.: 3 / Mutation: C40A, C82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: PML2BS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)[PLYSE] / References: UniProt: P11540
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 27030 / Num. obs: 27030 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.9
Reflection shellResolution: 2.3→2.34 Å / % possible all: 91.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→14.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 363326.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2632 9.9 %RANDOM
Rwork0.2 ---
obs0.2 26494 86.9 %-
all-26494 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.5631 Å2 / ksol: 0.395059 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.15 Å20 Å25.76 Å2
2--4.14 Å20 Å2
3----12.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4783 0 0 498 5281
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 418 9.4 %
Rwork0.229 4027 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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