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- PDB-2rbi: STRUCTURE OF BINASE MUTANT HIS 101 ASN -

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Basic information

Entry
Database: PDB / ID: 2rbi
TitleSTRUCTURE OF BINASE MUTANT HIS 101 ASN
ComponentsRIBONUCLEASE
KeywordsENDORIBONUCLEASE / MICROBIAL EXTRACELLULAR RIBONUCLEASE / PHOSPHODIESTER TRANSFERASE / HYDROLASE
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 intermedius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOffen, W.A. / Okorokov, A.L.
CitationJournal: Protein Eng. / Year: 1997
Title: RNA cleavage without hydrolysis. Splitting the catalytic activities of binase with Asn101 and Thr101 mutations.
Authors: Okorokov, A.L. / Panov, K.I. / Offen, W.A. / Mukhortov, V.G. / Antson, A.A. / Karpeisky, M.Y.a. / Wilkinson, A.J. / Dodson, G.G.
History
DepositionNov 12, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE
B: RIBONUCLEASE


Theoretical massNumber of molelcules
Total (without water)24,4072
Polymers24,4072
Non-polymers00
Water4,125229
1
A: RIBONUCLEASE


Theoretical massNumber of molelcules
Total (without water)12,2041
Polymers12,2041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBONUCLEASE


Theoretical massNumber of molelcules
Total (without water)12,2041
Polymers12,2041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.260, 69.150, 33.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBONUCLEASE / BINASE / EXTRACELLULAR RIBONUCLEASE FROM BACILLUS INTERMEDIUS


Mass: 12203.579 Da / Num. of mol.: 2 / Mutation: H101N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus intermedius (bacteria) / Strain: 7P
Description: BINASE GENE CO-EXPRESSED AS FUSION PROTEIN WITH ALKALINE PHOSPHATASE TO ENABLE EXPORT INTO PERIPLASMIC SPACE
Gene: PHOA-BINASE HIS101ASN / Plasmid: PEXBINN101 / Gene (production host): PHOA-BINASE HIS101ASN / Production host: Escherichia coli (E. coli)
Strain (production host): EPICURIAN COLI STRAIN XL-1 BLUE MRF'
References: UniProt: P00649, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: VAPOR DIFFUSION METHOD, WITH 12MG/ML BINASE HIS101ASN, 40MM GLYCINE PH 7.5, 8.75% POLYETHYL- ENE GLYCOL MR 10,000 AND 2.5% SATURATED SODIUM CITRATE IN THE HANGING DROP, AND 17.5% PEG 10,000, ...Details: VAPOR DIFFUSION METHOD, WITH 12MG/ML BINASE HIS101ASN, 40MM GLYCINE PH 7.5, 8.75% POLYETHYL- ENE GLYCOL MR 10,000 AND 2.5% SATURATED SODIUM CITRATE IN THE HANGING DROP, AND 17.5% PEG 10,000, 60MM GLYCINE PH 7.5 AND 5% SODIUM CITRATE IN WELL. LEFT FOR 2 DAYS AT 18 DEGREES CENTIGRADE., vapor diffusion, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlbinase H101N1drop
240 mMglycine1drop
317.5 %PEG100001drop
42.5 %satsodium citrate1drop
517.5 %PEG100001reservoir
660 mMglycine1reservoir
75 %sodium citrate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 22, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 13288 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.8 / % possible all: 80.7
Reflection
*PLUS
Num. measured all: 51822
Reflection shell
*PLUS
% possible obs: 80.7 %

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Processing

Software
NameVersionClassification
CCP4model building
PROLSQrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE BINASE

Resolution: 2.2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.178 --
obs-13096 97 %
Displacement parametersBiso mean: 27.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 0 229 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0390.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.5994
X-RAY DIFFRACTIONp_mcangle_it3.6876
X-RAY DIFFRACTIONp_scbond_it6.1038
X-RAY DIFFRACTIONp_scangle_it810
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1550.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.2650.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2270.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.2270.3
X-RAY DIFFRACTIONp_planar_tor2.7035
X-RAY DIFFRACTIONp_staggered_tor15.6220
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor14.88130
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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