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- PDB-1b21: DELETION OF A BURIED SALT BRIDGE IN BARNASE -

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Basic information

Entry
Database: PDB / ID: 1b21
TitleDELETION OF A BURIED SALT BRIDGE IN BARNASE
ComponentsPROTEIN (BARNASE)
KeywordsHYDROLASE / MICROBIAL RIBONUCLEASE / ALPHA/BETA PROTEIN
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 / Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 Å
AuthorsVaughan, C.K. / Harryson, P. / Buckle, A.M. / Oliveberg, M. / Fersht, A.R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: A structural double-mutant cycle: estimating the strength of a buried salt bridge in barnase.
Authors: Vaughan, C.K. / Harryson, P. / Buckle, A.M. / Fersht, A.R.
#1: Journal: Nature / Year: 1982
Title: Molecular Structure of a New Family of Ribonucleases
Authors: Mauguen, Y. / Hartley, R.W. / Dodson, E.J. / Dodson, G.G. / Bricogne, G. / Chothia, C. / Jack, A.
History
DepositionDec 3, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.name
Revision 1.4Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: 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: PROTEIN (BARNASE)
B: PROTEIN (BARNASE)
C: PROTEIN (BARNASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0484
Polymers36,9833
Non-polymers651
Water6,107339
1
A: PROTEIN (BARNASE)


Theoretical massNumber of molelcules
Total (without water)12,3281
Polymers12,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (BARNASE)


Theoretical massNumber of molelcules
Total (without water)12,3281
Polymers12,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN (BARNASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3932
Polymers12,3281
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.780, 57.780, 81.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.74748, 0.658167, 0.089941), (0.657333, -0.752383, 0.042806), (0.095844, 0.027124, -0.995027)1.0304, 72.6382, 100.0443
2given(0.562404, 0.822837, 0.081494), (0.821185, -0.567353, 0.061365), (0.09673, 0.032409, -0.994783)-5.2103, 33.299, 80.4385

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Components

#1: Protein PROTEIN (BARNASE)


Mass: 12327.620 Da / Num. of mol.: 3 / Mutation: R69S, D93N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Cellular location: EXTRACELLULARGlossary of biology / Plasmid: PMT410 / Production host: Escherichia coli (E. coli) / References: UniProt: P00648, EC: 3.1.27.3
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.11 Å3/Da / Density % sol: 42 %
Description: THE STRUCTURE WAS SOLVED BY RIGID BODY REFINEMENT USING WILD-TYPE BARNASE AS THE STARTING MODEL
Crystal growpH: 7.5
Details: DROP: 8-12 MG/ML PROTEIN 6 MM ZNSO4 0.6 M (NH4)2SO4 WELL: 2.58-2.73 M AMMONIUM PHOSPHATE BUFFER, PH 7.5 1-2 MM ZNSO4 0.15-0.30 M (NH4)2SO4 5-10 MM NH4OH
Components of the solutions
IDNameCrystal-IDSol-ID
1ZN SULFATE11
2NH4 SULFATE11
3ZN SULFATE12
4NH4 SULFATE12
5NH4OH12
6NH4 PHOSPHATE12
Crystal grow
*PLUS
Temperature: 288 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18-12 mg/mlprotein1drop
26 mM1dropZnSO4
30.1 Mammonium sulfate1drop
42.58-2.73 Mammonium phosphate1reservoir
51-2 mM1reservoirZn2SO4
60.15-0.30 Mammonium sulfate1reservoir
75-10 mM1reservoirNH4OH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: SUPER DOUBLE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→21.32 Å / Num. obs: 18526 / % possible obs: 91.4 % / Redundancy: 1.8 % / Biso Wilson estimate: 12.67 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.06
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 5.1 / % possible all: 59.3
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 59.3 % / Rmerge(I) obs: 0.144

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Processing

Software
NameVersionClassification
X-PLORmodel building
REFMACrefinement
iMOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2→19 Å / SU B: 5.81 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.268 -5 %
Rwork0.188 --
obs-16993 91.4 %
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 2→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 1 339 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.02
X-RAY DIFFRACTIONp_angle_d0.0220.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0190.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8212
X-RAY DIFFRACTIONp_mcangle_it1.3693
X-RAY DIFFRACTIONp_scbond_it0.792
X-RAY DIFFRACTIONp_scangle_it1.2383
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0840.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2350.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1490.3
X-RAY DIFFRACTIONp_planar_tor3.37
X-RAY DIFFRACTIONp_staggered_tor16.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor17.720
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.188 / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.3 Å2

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