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- PDB-1o57: CRYSTAL STRUCTURE OF THE PURINE OPERON REPRESSOR OF BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1o57
TitleCRYSTAL STRUCTURE OF THE PURINE OPERON REPRESSOR OF BACILLUS SUBTILIS
ComponentsPUR OPERON REPRESSOR
KeywordsDNA BINDING PROTEIN / PURINE OPERON REPRESSOR / HELIX-TURN-HELIX DOMAIN / PHOSPHORIBOSYLTRANSEFERASES / DOMAIN RECOMBINATION / DNA BINDING / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


negative regulation of purine nucleobase metabolic process / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Pur operon repressor / Bacterial purine repressor, N-terminal / Bacterial purine repressor, N-terminal / : / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Pur operon repressor / Bacterial purine repressor, N-terminal / Bacterial purine repressor, N-terminal / : / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pur operon repressor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsSinha, S.C. / Krahn, J. / Shin, B.S. / Tomchick, D.R. / Zalkin, H. / Smith, J.L.
CitationJournal: J.Bacteriol. / Year: 2003
Title: The Purine Repressor of Bacillus Subtilis: A Novel Combination of Domains Adapted for Transcription Regulation
Authors: Sinha, S.C. / Krahn, J. / Shin, B.S. / Tomchick, D.R. / Zalkin, H. / Smith, J.L.
History
DepositionApr 20, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionAug 26, 2003ID: 1P41
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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: PUR OPERON REPRESSOR
B: PUR OPERON REPRESSOR
C: PUR OPERON REPRESSOR
D: PUR OPERON REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,25420
Polymers128,3594
Non-polymers2,89516
Water10,233568
1
A: PUR OPERON REPRESSOR
B: PUR OPERON REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,69310
Polymers64,1802
Non-polymers1,5148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-63 kcal/mol
Surface area23010 Å2
MethodPISA
2
C: PUR OPERON REPRESSOR
D: PUR OPERON REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,56110
Polymers64,1802
Non-polymers1,3818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-76 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.077, 72.156, 82.967
Angle α, β, γ (deg.)84.75, 84.03, 67.47
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PUR OPERON REPRESSOR


Mass: 32089.771 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PURR / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P37551

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Non-polymers , 7 types, 584 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.8 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10mg/mL PurR, 83 mM HEPES, pH 7.0, 5% PEG8000, 450 mM Lithium sulfate, 50 mM ammonium sulfate, 300 mM NaCl, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMHEPES1droppH8.0
350 mMammonium sulfate1drop
4300 mM1dropNaCl
55 %PEG80001reservoir
666.7 mMHEPES1reservoirpH7.0
7167 mM1reservoirLi2SO4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9790, 0.9788, 1.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATESep 1, 1997
RIGAKU RAXIS IIC2IMAGE PLATESep 1, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97881
31.54181
ReflectionResolution: 2→20 Å / Num. obs: 66722 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 45.3 Å2 / Rsym value: 0.073 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.28 Å / Redundancy: 1 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.194 / % possible all: 96.6
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 96.6 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1384607.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: NCS RESTRAINTS WERE USED IN ALL BUT THE FINAL CYCLES OF REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3335 5 %RANDOM
Rwork0.188 ---
obs0.1 66365 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.05 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 52.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å22.47 Å2-0.65 Å2
2--0.88 Å20.16 Å2
3----2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8383 0 181 568 9132
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.394.5
X-RAY DIFFRACTIONc_mcangle_it65
X-RAY DIFFRACTIONc_scbond_it7.86
X-RAY DIFFRACTIONc_scangle_it9.747.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 515 4.9 %
Rwork0.233 9938 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3LIGANDS.PARLIGANDS.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 4.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.459
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93

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