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- PDB-1b2z: DELETION OF A BURIED SALT BRIDGE IN BARNASE -

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Basic information

Entry
Database: PDB / ID: 1b2z
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 / 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 / OTHER / Resolution: 2.03 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 / 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 / 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_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.ptnr1_symmetry / _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.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_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)37,2594
Polymers37,1933
Non-polymers651
Water6,377354
1
A: PROTEIN (BARNASE)


Theoretical massNumber of molelcules
Total (without water)12,3981
Polymers12,3981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (BARNASE)


Theoretical massNumber of molelcules
Total (without water)12,3981
Polymers12,3981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN (BARNASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4632
Polymers12,3981
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.750, 57.750, 81.280
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(0.752059, 0.65253, 0.092798), (0.651599, -0.757274, 0.044217), (0.099127, 0.027213, -0.994703)0.9808, 72.7143, 100.8196
2given(0.572214, 0.816791, 0.07365), (0.815383, -0.576243, 0.055625), (0.087875, 0.028223, -0.995732)-5.0507, 33.8035, 81.7592

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Components

#1: Protein PROTEIN (BARNASE)


Mass: 12397.736 Da / Num. of mol.: 3 / Mutation: D93N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Cellular location: EXTRACELLULAR / 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


Mass: 18.015 Da / Num. of mol.: 354 / 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 %
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: Nov 1, 1995 / 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: 2.03→18.42 Å / Num. obs: 18864 / % possible obs: 96.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 15.12 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.73
Reflection shellResolution: 2.03→2.05 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 5.29 / % possible all: 72.2
Reflection shell
*PLUS
% possible obs: 72.2 %

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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: 2.03→18.38 Å / SU B: 4.89 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.228 -5 %
Rwork0.17 --
obs-17900 96.2 %
Displacement parametersBiso mean: 17.39 Å2
Refinement stepCycle: LAST / Resolution: 2.03→18.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 1 354 2940
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4612
X-RAY DIFFRACTIONp_mcangle_it2.2153
X-RAY DIFFRACTIONp_scbond_it1.6592
X-RAY DIFFRACTIONp_scangle_it2.4143
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0970.15
X-RAY DIFFRACTIONp_singtor_nbd0.1680.3
X-RAY DIFFRACTIONp_multtor_nbd0.2480.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1570.3
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor14.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor17.420
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.27

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