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- PDB-2fxa: Structure of the Protease Production Regulatory Protein hpr from ... -

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Basic information

Entry
Database: PDB / ID: 2fxa
TitleStructure of the Protease Production Regulatory Protein hpr from Bacillus subtilis.
ComponentsProtease production regulatory protein hpr
KeywordsTRANSCRIPTION / Bacillus subtilis / hpr / protease porduction / regulation / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


response to stress / sporulation resulting in formation of a cellular spore / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
HTH-type transcriptional regulator Hpr / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...HTH-type transcriptional regulator Hpr / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / DNA-binding transcriptional repressor ScoC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCuff, M.E. / Skarina, T. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the Protease Production Regulatory Protein hpr from Bacillus subtilis.
Authors: Cuff, M.E. / Skarina, T. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionFeb 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 9, 2015Group: Data collection
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Protease production regulatory protein hpr
B: Protease production regulatory protein hpr
C: Protease production regulatory protein hpr
D: Protease production regulatory protein hpr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,42022
Polymers97,6424
Non-polymers1,77818
Water3,189177
1
A: Protease production regulatory protein hpr
B: Protease production regulatory protein hpr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,96214
Polymers48,8212
Non-polymers1,14112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-43 kcal/mol
Surface area16230 Å2
MethodPISA
2
C: Protease production regulatory protein hpr
D: Protease production regulatory protein hpr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4588
Polymers48,8212
Non-polymers6376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-42 kcal/mol
Surface area15600 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20710 Å2
ΔGint-95 kcal/mol
Surface area29280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.272, 79.909, 131.239
Angle α, β, γ (deg.)90.00, 100.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Protease production regulatory protein hpr


Mass: 24410.537 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: hpr, catA, scoC / Plasmid: p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P11065

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Non-polymers , 5 types, 195 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5
Details: 0.2M K/Na tartrate tetrahydrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97887, 0.97943
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 5, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978871
20.979431
ReflectionResolution: 2.4→50 Å / Num. all: 41448 / Num. obs: 41448 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.5 Å / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.934 / SU B: 13.777 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.315 / ESU R Free: 0.223
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23392 2095 5.1 %RANDOM
Rwork0.2081 ---
all0.20945 39352 --
obs0.20945 39352 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.709 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20.99 Å2
2--3.13 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5443 0 117 177 5737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225943
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9397999
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7425693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.37624.248306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.281151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2051525
X-RAY DIFFRACTIONr_chiral_restr0.1060.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024502
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.22790
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24079
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4051.53450
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.625445
X-RAY DIFFRACTIONr_scbond_it2.63132891
X-RAY DIFFRACTIONr_scangle_it3.9074.52545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 152 -
Rwork0.227 2845 -
obs--97.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8499-1.7154-0.10743.54341.17161.3929-0.1241-0.2699-0.31550.16840.2810.0599-0.00030.2413-0.1569-0.2941-0.0366-0.0133-0.262-0.0421-0.239117.550321.498714.0196
22.8639-1.01340.46912.6043-2.24222.9004-0.060.01620.57360.28010.1487-0.0412-0.2065-0.1103-0.0888-0.2942-0.02150.0205-0.27970.0008-0.18424.298940.28038.7974
33.0198-0.2253-1.48551.68771.7633.1196-0.0033-0.41090.2145-0.2075-0.19520.5677-0.4117-0.28040.19850.03980.1318-0.0085-0.0367-0.1039-0.1295-4.746843.789250.2196
42.5891-0.6681.67652.5561-1.73343.3622-0.072-0.6237-0.32880.3623-0.068-0.5342-0.15090.15520.140.03480.07120.01190.0270.1123-0.14348.718527.22954.7566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1678 - 169
2X-RAY DIFFRACTION2BB8 - 18710 - 189
3X-RAY DIFFRACTION3CC8 - 16710 - 169
4X-RAY DIFFRACTION4DD7 - 1699 - 171

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