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- PDB-3qk7: Crystal structure of putative Transcriptional regulator from Yers... -

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Basic information

Entry
Database: PDB / ID: 3qk7
TitleCrystal structure of putative Transcriptional regulator from Yersinia pestis biovar Microtus str. 91001
ComponentsTranscriptional regulatorsRegulation of gene expression
KeywordsTRANSCRIPTION REGULATOR / STRUCTURAL GENOMICS / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / transcriptional regulator / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold ...Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulators / Transcriptional regulators
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.7 Å
AuthorsMalashkevich, V.N. / Toro, R. / 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 putative Transcriptional regulator from Yersinia pestis biovar Microtus str. 91001
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJan 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulators
B: Transcriptional regulators
C: Transcriptional regulators


Theoretical massNumber of molelcules
Total (without water)97,6843
Polymers97,6843
Non-polymers00
Water1,53185
1
A: Transcriptional regulators

A: Transcriptional regulators


Theoretical massNumber of molelcules
Total (without water)65,1222
Polymers65,1222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
Buried area3130 Å2
ΔGint-13 kcal/mol
Surface area24280 Å2
MethodPISA
2
B: Transcriptional regulators
C: Transcriptional regulators


Theoretical massNumber of molelcules
Total (without water)65,1222
Polymers65,1222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-14 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.700, 96.700, 256.118
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Transcriptional regulators / Regulation of gene expression


Mass: 32561.184 Da / Num. of mol.: 3 / Fragment: Sequence database residues 67-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: 91001 / Gene: purR3, YP_070137.1, YP_1471 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q74V61, UniProt: A0A0H2W507*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% iso-propanol, 0.1 M Na-Hepes, 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 5.3 % / Av σ(I) over netI: 18.45 / Number: 336002 / Rmerge(I) obs: 0.113 / Χ2: 1.61 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 63658 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.325099.610.053.335.3
5.817.3299.910.0672.4875.4
5.085.8199.910.0672.2015
4.625.0810010.0682.3625.2
4.294.6210010.0742.4235.2
4.034.2910010.0852.2575.2
3.834.0310010.0971.9395.3
3.663.8310010.1141.5485.3
3.523.6610010.1291.3745.3
3.43.5210010.1521.355.4
3.33.410010.2041.1635.3
3.23.310010.2581.0885.3
3.123.210010.3261.0785.3
3.043.1210010.3931.0615.3
2.973.0410010.4431.0755.3
2.912.9710010.5461.0745.3
2.852.9199.910.6591.1045.3
2.82.8599.910.7461.0795.3
2.752.899.910.9241.0745.3
2.72.7599.911.1515.2
ReflectionResolution: 2.7→50 Å / Num. obs: 63658 / % possible obs: 100 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.113 / Χ2: 1.606 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.7-2.755.231901.15199.9
2.75-2.85.331241.07499.90.924
2.8-2.855.332771.07999.90.746
2.85-2.915.331301.10499.90.659
2.91-2.975.332001.0741000.546
2.97-3.045.331731.0751000.443
3.04-3.125.332111.0611000.393
3.12-3.25.331291.0781000.326
3.2-3.35.331871.0881000.258
3.3-3.45.332051.1631000.204
3.4-3.525.431411.351000.152
3.52-3.665.331911.3741000.129
3.66-3.835.332101.5481000.114
3.83-4.035.332151.9391000.097
4.03-4.295.231492.2571000.085
4.29-4.625.231742.4231000.074
4.62-5.085.231952.3621000.068
5.08-5.81531832.20199.90.067
5.81-7.325.431802.48799.90.067
7.32-505.331943.3399.60.05

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→19.74 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.3003 / WRfactor Rwork: 0.2337 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7075 / SU B: 34.017 / SU ML: 0.303 / SU R Cruickshank DPI: 0.9073 / SU Rfree: 0.3904 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.907 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2991 1574 5 %RANDOM
Rwork0.2336 ---
obs0.2368 31187 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 86.59 Å2 / Biso mean: 68.278 Å2 / Biso min: 14.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 0 85 6567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226611
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9898984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72424.056286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.057151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1121549
X-RAY DIFFRACTIONr_chiral_restr0.0860.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215004
X-RAY DIFFRACTIONr_mcbond_it0.7723.54178
X-RAY DIFFRACTIONr_mcangle_it3.991506710
X-RAY DIFFRACTIONr_scbond_it10.003502433
X-RAY DIFFRACTIONr_scangle_it0.6524.52274
LS refinement shellResolution: 2.701→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.975 117 -
Rwork0.01 2031 -
all-2148 -
obs--91.99 %
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)
11.2890.09350.31241.12750.88875.0396-0.1379-0.327-0.25030.0709-0.16710.16190.48270.03370.3050.07380.0660.0970.28930.12880.304-0.353633.2662150.1093
21.64940.2585-0.06753.6048-0.41671.3397-0.1189-0.28120.16950.02860.24610.18-0.114-0.143-0.12710.02020.0470.00140.2755-0.01810.072935.39556.0055145.317
32.0931.19870.04123.56820.66971.4149-0.10970.26580.1382-0.42930.08730.0654-0.22370.08060.02240.1806-0.0052-0.05170.21590.11320.081627.348655.9718116.4768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999

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