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- PDB-2f56: Barnase cross-linked with glutaraldehyde soaked in 6M urea -

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Basic information

Entry
Database: PDB / ID: 2f56
TitleBarnase cross-linked with glutaraldehyde soaked in 6M urea
ComponentsRibonuclease
KeywordsHYDROLASE / DENATURATION / LYSOZYME / BARNASE / CROSS-LINKED CRYSTALS / GLUTARALDEHYDE / UREA / THIOUREA / BROMOETHANOL
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region
Similarity search - Function
: / Barnase / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.955 Å
AuthorsPrange, T. / Salem, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2006
Title: On the edge of the denaturation process: Application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations.
Authors: Salem, M. / Mauguen, Y. / Prange, T.
History
DepositionNov 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2012Group: Refinement description
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 23, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Ribonuclease
B: Ribonuclease
C: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,32515
Polymers36,5993
Non-polymers72612
Water4,252236
1
A: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3804
Polymers12,2001
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5607
Polymers12,2001
Non-polymers3606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3854
Polymers12,2001
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Ribonuclease
hetero molecules

C: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7658
Polymers24,3992
Non-polymers3666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-y,x-y+1,z-1/31
Buried area1290 Å2
ΔGint-26 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.280, 59.280, 81.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Ribonuclease / Barnase / RNase Ba


Mass: 12199.515 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: PMJ1002 / Production host: Escherichia coli (E. coli)
References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH4N2O
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: AMMONIUM SULFATE, HEPES BUFFER. PROTEIN 20 MG/ML, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 25, 2002 / Details: CURVATED MULTILAYER MIRROR
RadiationMonochromator: CURVATED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.955→10 Å / Num. all: 23026 / Num. obs: 21767 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Net I/σ(I): 22
Reflection shellResolution: 1.955→2.1 Å / Mean I/σ(I) obs: 10.7 / % possible all: 99.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXLrefinement
SHELXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2F4Y

2f4y


Resolution: 1.955→10 Å / Num. parameters: 11467 / Num. restraintsaints: 10750 / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
Rwork0.1621 --
all-23026 -
obs-21767 100 %
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2442 / Occupancy sum non hydrogen: 2840
Refinement stepCycle: LAST / Resolution: 1.955→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 45 236 2861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.325
X-RAY DIFFRACTIONs_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used% reflection obs (%)
1.955-2.10.167X-RAY DIFFRACTION4130587.4
2.1-2.50.147X-RAY DIFFRACTION7138593.3
2.5-30.134X-RAY DIFFRACTION4328596.7
3-80.166X-RAY DIFFRACTION5893599.3
8-100.352X-RAY DIFFRACTION1775100

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