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- PDB-3kch: Baranase crosslinked by glutaraldehyde -

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Basic information

Entry
Database: PDB / ID: 3kch
TitleBaranase crosslinked by glutaraldehyde
ComponentsRibonuclease
KeywordsHYDROLASE / ribonuclease / microbial ribonuclease / glutaraldehyde / crosslink / Endonuclease / Nuclease / Secreted
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
PENTANEDIAL / Ribonuclease
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsPrange, T. / Salem, M. / Mauguen, Y.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Revisiting glutaraldehyde cross-linking: the case of the Arg-Lys intermolecular doublet
Authors: Salem, M. / Mauguen, Y. / Prange, T.
#1: Journal: 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
DepositionOct 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Nov 1, 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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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)37,4976
Polymers37,1963
Non-polymers3003
Water4,612256
1
A: Ribonuclease
hetero molecules

A: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9984
Polymers24,7972
Non-polymers2002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-y,x-y,z-1/31
2
B: Ribonuclease
hetero molecules

B: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9984
Polymers24,7972
Non-polymers2002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z+1/31
3
C: Ribonuclease
hetero molecules

C: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9984
Polymers24,7972
Non-polymers2002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x+y-1,-x,z+1/31
Unit cell
Length a, b, c (Å)58.970, 58.970, 82.140
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: 12398.721 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-PTD / PENTANEDIAL / Glutaraldehyde


Mass: 100.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.216787 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG 1000, HEPES, glutaraldehyde, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.964 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 2002 / Details: Bent mirror, Si(111) monochromator
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.94→20 Å / Num. all: 22894 / Num. obs: 22894 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 18.2
Reflection shellResolution: 1.94→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 4.6 / Num. unique all: 4661 / Rsym value: 0.171 / % possible all: 93.7

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Processing

Software
NameClassification
MAR345dtbdata collection
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1A2P

1a2p


Resolution: 1.94→20 Å / Num. parameters: 11455 / Num. restraintsaints: 10682 / Cross valid method: FREE R / σ(F): 2 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 1130 5 %RANDOM
Rwork0.1455 ---
all0.1483 22894 --
obs0.1455 22107 97.8 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2863
Refinement stepCycle: LAST / Resolution: 1.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 15 256 2863
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.015
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.014
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.023
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.07
X-RAY DIFFRACTIONs_approx_iso_adps0

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