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- PDB-1a2p: BARNASE WILDTYPE STRUCTURE AT 1.5 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1a2p
TitleBARNASE WILDTYPE STRUCTURE AT 1.5 ANGSTROMS RESOLUTION
ComponentsBARNASE
KeywordsRIBONUCLEASE / 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 / SYNCHROTRON / Resolution: 1.5 Å
AuthorsMartin, C. / Richard, V. / Salem, M. / Hartley, R.W. / Mauguen, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Refinement and structural analysis of barnase at 1.5 A resolution.
Authors: Martin, C. / Richard, V. / Salem, M. / Hartley, R. / Mauguen, Y.
History
DepositionJan 7, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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_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_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

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Assembly

Deposited unit
A: BARNASE
B: BARNASE
C: BARNASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3926
Polymers37,1963
Non-polymers1963
Water7,476415
1
A: BARNASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4642
Polymers12,3991
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BARNASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4642
Polymers12,3991
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BARNASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4642
Polymers12,3991
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.970, 58.970, 81.580
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(0.75779, 0.64748, 0.08078), (0.64621, -0.76186, 0.04446), (0.09033, 0.01851, -0.99574)-58.48021, 51.57518, 98.15767
2given(0.58987, 0.80583, 0.05186), (0.80311, -0.59214, 0.06619), (0.08405, 0.0026, -0.99646)-30.43273, 20.75484, 81.77702

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Components

#1: Protein BARNASE


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-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein1drop
23.0 Mammonium sulfate1drop
30.03 Mzinc sulfate1drop
41.9 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: MULTILAYER MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.5→19.9 Å / Num. obs: 48463 / % possible obs: 96.9 % / Redundancy: 2.5 % / Rsym value: 0.038 / Net I/σ(I): 11.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.158 / % possible all: 94.5
Reflection
*PLUS
Rmerge(I) obs: 0.038

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Processing

Software
NameClassification
SHELXL-93model building
X-PLORmodel building
SHELXL-93refinement
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
SHELXL-93phasing
X-PLORphasing
RefinementResolution: 1.5→8 Å / Num. parameters: 27377 / Num. restraintsaints: 33057 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.5 ANGSTROMS. AT R-VALUES OF R=0.174 FOR F.GREATER THAN 3 ...Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.5 ANGSTROMS. AT R-VALUES OF R=0.174 FOR F.GREATER THAN 3 SIGMA(F), THE REFINEMENT WAS CONTINUED WITH THE PROGRAM SHELXL-93. ANISOU RECORDS CONTAIN ANISOTROPIC DISPLACEMENT PARAMETERS U11 U22 U33 U23 U13 U12 (ANGSTROMS**2) MULTIPLIED BY 10000. ISOTROPIC EQUIVALENTS OF ANISOTROPIC TEMPERATURE FACTORS ARE ALSO PRESENTED IN THIS ENTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.174 4812 10 %EVERY 10TH REFLECTION
all0.115 48118 --
obs0.111 -95.4 %-
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 2417.5 / Occupancy sum non hydrogen: 2972
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2624 0 3 415 3042
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d1.76
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.273
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.2
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.01
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0.1

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