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- PDB-2f5w: Cross-linked barnase soaked in 3 M thiourea -

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Basic information

Entry
Database: PDB / ID: 2f5w
TitleCross-linked barnase soaked in 3 M thiourea
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
THIOUREA / Ribonuclease
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.001 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 28, 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
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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)36,7405
Polymers36,5993
Non-polymers1422
Water2,828157
1
A: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)12,2001
Polymers12,2001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)12,2001
Polymers12,2001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3413
Polymers12,2001
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.500, 59.500, 81.510
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TOU / THIOUREA


Mass: 76.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PROTEIN 20 MG/ML, AMMONIUM SULFATE, ZINC CHLORIDE, HEPES BUFFER, 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 24, 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: 2.001→10 Å / Num. all: 21481 / Num. obs: 17459 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4
Reflection shellResolution: 2.001→2.1 Å / Mean I/σ(I) obs: 4.1 / % possible all: 97.7

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Processing

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

2f4y


Resolution: 2.001→10 Å / Num. parameters: 11015 / Num. restraintsaints: 10731 / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rwork0.1864 --
all-21481 -
obs-17459 99.2 %
Refine analyzeOccupancy sum hydrogen: 2469 / Occupancy sum non hydrogen: 2753
Refinement stepCycle: LAST / Resolution: 2.001→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 5 157 2754
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.312
X-RAY DIFFRACTIONs_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_anti_bump_dis_restr
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 (%)
2.001-2.10.187X-RAY DIFFRACTION2702554.6
2.1-2.50.175X-RAY DIFFRACTION7288573.6
2.5-30.155X-RAY DIFFRACTION4424587
3-80.17X-RAY DIFFRACTION5694597.1
8-100.402X-RAY DIFFRACTION174550

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