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- PDB-1qd9: Bacillus subtilis YABJ -

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Basic information

Entry
Database: PDB / ID: 1qd9
TitleBacillus subtilis YABJ
ComponentsPURINE REGULATORY PROTEIN YABJ
KeywordsGENE REGULATION / PERCHLORIC ACID SOLUBLE PROTEIN / PURINE REGULATION / YJGF/YER057C FAMILY
Function / homology
Function and homology information


2-oxobutyrate biosynthetic process / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate/2-iminopropanoate deaminase / : / deaminase activity / isoleucine biosynthetic process / response to toxic substance / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / ETHYL MERCURY ION / : / 2-iminobutanoate/2-iminopropanoate deaminase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / HG MAD / Resolution: 1.7 Å
AuthorsSmith, J.L. / Sinha, S. / Rappu, P. / Lange, S.C. / Mantsala, P. / Zalkin, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family.
Authors: Sinha, S. / Rappu, P. / Lange, S.C. / Mantsala, P. / Zalkin, H. / Smith, J.L.
History
DepositionJul 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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_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: PURINE REGULATORY PROTEIN YABJ
B: PURINE REGULATORY PROTEIN YABJ
C: PURINE REGULATORY PROTEIN YABJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,62912
Polymers40,6093
Non-polymers1,0209
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-60 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.350, 53.350, 204.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0631, -0.4353, 0.8981), (0.8603, -0.4323, -0.27), (0.5058, -0.7897, 0.3472)
Vector: -29.4543, 18.498, 18.3962)
DetailsTHE MODEL INCLUDES RESIDUES 2 - 125 IN EACH SUBUNIT. N-TERMINAL SEQUENCE ANALYSIS INDICATED THAT MET1 WAS NOT PRESENT IN THE PURIFIED PROTEIN USED FOR CRYSTALLIZATION. YABJ IS A TRIMER. SUBUNITS IN THE TRIMER ARE RELATED BY NCS THREE-FOLD ROTATIONAL SYMMETRY. THE ASYMMETRIC UNIT CONTAINS ONE TRIMER OF YABJ.

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Components

#1: Protein PURINE REGULATORY PROTEIN YABJ


Mass: 13536.371 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PLYSS / References: UniProt: P37552
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5Hg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.04 Å3/Da / Density % sol: 40 %
Crystal growpH: 4.6
Details: SODIUM PHOSPHATE, PEG 4000, AMMONIUM SULPHATE, SODIUM ACETATE., pH 4.60
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16.3 mg/mlprotein1drop
240 mMsodium phosphate1droppH7.4
320 %PEG40001reservoir
40.45 Mammonium acetate1reservoir
50.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.0095
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 11, 1998
RadiationProtocol: MULTIPLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0095 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 309290 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 8.7 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 8.6 / % possible all: 90.7
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Num. obs: 35377 / Observed criterion σ(I): 1 / Redundancy: 8.7 %
Reflection shell
*PLUS
% possible obs: 95.6 % / Redundancy: 4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS0.5refinement
RefinementMethod to determine structure: HG MAD / Resolution: 1.7→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2121779.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT TARGET EQUALS MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES AND PHASE PROBABILITY DISTRIBUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1759 5.1 %RANDOM
Rwork0.166 ---
obs0.166 34805 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 86.61 Å2 / ksol: 0.456 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20.82 Å20 Å2
2--1.53 Å20 Å2
3----3.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 14 498 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it4.8610
X-RAY DIFFRACTIONc_scangle_it6.2410.5
Refine LS restraints NCSNCS model details: NONE FOR FINAL REFINEMENT
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.234 150 4.6 %
Rwork0.195 3129 -
obs--90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ACY.PARACY.TOP
X-RAY DIFFRACTION4HGLIGS.PARHGLIGS.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it10
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it10.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.234 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.195

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