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- PDB-2pju: Crystal structure of propionate catabolism operon regulatory prot... -

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Basic information

Entry
Database: PDB / ID: 2pju
TitleCrystal structure of propionate catabolism operon regulatory protein prpR
ComponentsPropionate catabolism operon regulatory protein
KeywordsTRANSCRIPTION / structural genomics / prpR / transcriptional regulation / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


propionate catabolic process, 2-methylcitrate cycle / phosphorelay response regulator activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / response to radiation / protein-DNA complex / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / ATP hydrolysis activity ...propionate catabolic process, 2-methylcitrate cycle / phosphorelay response regulator activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / response to radiation / protein-DNA complex / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Signal transduction response regulator, propionate catabolism, transcriptional regulator PrpR / PrpR receptor domain-like / Signal transduction response regulator, propionate catabolism activator, N-terminal / Propionate catabolism activator / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain ...Signal transduction response regulator, propionate catabolism, transcriptional regulator PrpR / PrpR receptor domain-like / Signal transduction response regulator, propionate catabolism activator, N-terminal / Propionate catabolism activator / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Response regulator / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Propionate catabolism operon regulatory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsRamagopal, U.A. / Toro, R. / Gilmore, M. / Wu, B. / Koss, J. / Groshong, C. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of propionate catabolism operon regulatory protein prpR
Authors: Ramagopal, U.A. / Toro, R. / Gilmore, M. / Wu, B. / Koss, J. / Groshong, C. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.6Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.7Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Propionate catabolism operon regulatory protein
B: Propionate catabolism operon regulatory protein
C: Propionate catabolism operon regulatory protein
D: Propionate catabolism operon regulatory protein


Theoretical massNumber of molelcules
Total (without water)100,3074
Polymers100,3074
Non-polymers00
Water4,900272
1
A: Propionate catabolism operon regulatory protein
B: Propionate catabolism operon regulatory protein


Theoretical massNumber of molelcules
Total (without water)50,1532
Polymers50,1532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-19 kcal/mol
Surface area17840 Å2
MethodPISA
2
C: Propionate catabolism operon regulatory protein
D: Propionate catabolism operon regulatory protein


Theoretical massNumber of molelcules
Total (without water)50,1532
Polymers50,1532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-18 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.657, 58.545, 103.576
Angle α, β, γ (deg.)85.030, 88.560, 86.940
Int Tables number1
Space group name H-MP1
DetailsBiological unit appears to be dimer

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Components

#1: Protein
Propionate catabolism operon regulatory protein


Mass: 25076.641 Da / Num. of mol.: 4 / Mutation: A96F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12, MG1655 / Gene: prpR, b0330, JW0322 / Plasmid: BC-psSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P77743
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Hepes pH 7.5, 15% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9793
SYNCHROTRONAPS 31-ID20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 28, 2007
MAR CCD 165 mm2CCDMar 6, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21
ReflectionRedundancy: 2.5 % / Av σ(I) over netI: 7.2 / Number: 119318 / Rmerge(I) obs: 0.089 / Χ2: 1.22 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 47669 / % possible obs: 97.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.52509610.0822.9852.5
3.594.529910.0732.3092.5
3.143.5998.710.0821.8862.5
2.853.1498.510.0931.3792.5
2.652.8598.510.1150.9622.5
2.492.6598.210.1380.7182.6
2.372.4997.910.1610.5772.5
2.262.3797.910.1970.5052.4
2.182.2697.410.2480.4712.6
2.12.1897.310.3130.412.4
ReflectionResolution: 2.1→50 Å / Num. all: 47669 / Num. obs: 47669 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.089 / Χ2: 1.219 / Net I/σ(I): 7.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4671 / Rsym value: 0.296 / Χ2: 0.41 / % possible all: 97.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→37.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.285 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.239 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2436 5.1 %RANDOM
Rwork0.201 ---
all0.204 47666 --
obs0.204 47666 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0.18 Å2-0.41 Å2
2--1.34 Å20.44 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5946 0 0 272 6218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226042
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9658185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6695764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49823.622254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8121543
X-RAY DIFFRACTIONr_chiral_restr0.0950.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024456
X-RAY DIFFRACTIONr_nbd_refined0.2060.22618
X-RAY DIFFRACTIONr_nbtor_refined0.30.24208
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.212
X-RAY DIFFRACTIONr_mcbond_it0.7821.53920
X-RAY DIFFRACTIONr_mcangle_it1.24226139
X-RAY DIFFRACTIONr_scbond_it2.02132378
X-RAY DIFFRACTIONr_scangle_it3.1264.52046
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 173 -
Rwork0.229 3214 -
obs-3387 95.68 %
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)
11.8615-1.40190.46513.5375-1.1751.7957-0.1027-0.02870.010.27230.0508-0.1419-0.1951-0.02590.0519-0.1743-0.03220.0102-0.06570.0053-0.178527.998222.862689.4268
22.46630.53050.68563.56410.79072.2245-0.1705-0.06860.1133-0.22410.0941-0.1131-0.39990.14190.0764-0.1136-0.01470.008-0.077-0.0012-0.163640.614823.4699114.3102
31.96440.70530.37514.320.05971.0745-0.13240.00150.1248-0.26120.093-0.0372-0.22410.0210.0394-0.12160.02610.0245-0.1524-0.0132-0.191623.602748.686761.7756
41.6797-1.65820.79334.7559-1.88072.1042-0.14840.1165-0.01270.25660.0068-0.0389-0.19560.05270.1416-0.1369-0.04030.01340.0005-0.0265-0.12449.53752.8637141.8382
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA13 - 19615 - 198
22BB13 - 19715 - 199
33CC13 - 19815 - 200
44DD13 - 20415 - 206

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