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- PDB-3qkx: Crystal structure of a TetR-family transcriptional regulator (HI0... -

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Basic information

Entry
Database: PDB / ID: 3qkx
TitleCrystal structure of a TetR-family transcriptional regulator (HI0893) from Haemophilus influenzae RD at 2.35 A resolution
ComponentsUncharacterized HTH-type transcriptional regulator HI_0893
KeywordsTranscription regulator / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / TRANSCRIPTION
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
: / Tetracyclin repressor-like HI_0893, C-terminal domain / : / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. ...: / Tetracyclin repressor-like HI_0893, C-terminal domain / : / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized HTH-type transcriptional regulator HI_0893
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a TetR-family transcriptional regulator (HI0893) from Haemophilus influenzae RD at 2.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.5Nov 27, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized HTH-type transcriptional regulator HI_0893
B: Uncharacterized HTH-type transcriptional regulator HI_0893
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,70413
Polymers44,7762
Non-polymers92811
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-99 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.160, 71.160, 159.334
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEU6AA7 - 88 - 9
21ASPASPLEULEU6BB7 - 88 - 9
12ALAALAGLUGLU4AA9 - 5310 - 54
22ALAALAGLUGLU4BB9 - 5310 - 54
13LEULEUSERSER4AA54 - 10355 - 104
23LEULEUSERSER4BB54 - 10355 - 104
14ASNASNPROPRO2AA104 - 112105 - 113
24ASNASNPROPRO2BB104 - 112105 - 113
15ASNASNILEILE4AA113 - 121114 - 122
25ASNASNILEILE4BB113 - 121114 - 122
16LYSLYSPROPRO6AA122 - 171123 - 172
26LYSLYSPROPRO6BB122 - 171123 - 172
17GLUGLULYSLYS2AA172 - 187173 - 188
27GLUGLULYSLYS2BB172 - 187173 - 188
DetailsSTATIC LIGHT SCATTERING WITH ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Uncharacterized HTH-type transcriptional regulator HI_0893 / TetR-family transcriptional regulator


Mass: 22387.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI_0893 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: P44923
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (1-187) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (1-187) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.33
Details: 1.80 M lithium sulfate, 0.1M HEPES pH 7.33, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97954,0.91837,0.97917
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.918371
30.979171
ReflectionResolution: 2.35→29.56 Å / Num. all: 19028 / Num. obs: 19028 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 63.528 Å2 / Rsym value: 0.081 / Net I/σ(I): 13
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.35-2.417.71.61066713921.32299.9
2.41-2.487.71.91057213801.128100
2.48-2.557.72.31025213360.898100
2.55-2.637.73.1985212840.669100
2.63-2.717.73.9963112530.525100
2.71-2.817.75926112050.383100
2.81-2.917.76.9889411600.271100
2.91-3.037.78.3858111150.214100
3.03-3.177.711851511070.155100
3.17-3.327.713.7787410230.117100
3.32-3.57.717.475709830.085100
3.5-3.727.721.572569430.07100
3.72-3.977.725.568358870.06100
3.97-4.297.727.860947930.057100
4.29-4.77.731.258947660.054100
4.7-5.257.730.551806720.051100
5.25-6.077.729.345805980.062100
6.07-7.437.63039175160.069100
7.43-10.517.535.430214010.04999.7
10.51-29.567.236.315392140.04495.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALAdata scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→29.56 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 18.467 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.396 / ESU R Free: 0.247
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. THE MODELING OF MSE B65 IN DUAL CONFORMATION IS SUPPORTED BY THE ANOMALOUS DIFFERENCE FOURIER MAP. 6. RESIDUES 166-168 OF CHAIN A WERE NOT MODELED DUE TO POOR ELECTRON DENSITY IN THIS REGION. 7. ETHYLENE GLYCOL (EDO) AND SULFATE (SO4) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 8. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 979 5.2 %RANDOM
Rwork0.2227 ---
obs0.224 18989 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 153.22 Å2 / Biso mean: 69.5937 Å2 / Biso min: 28.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 49 47 3008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223117
X-RAY DIFFRACTIONr_bond_other_d0.0020.022103
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.9644231
X-RAY DIFFRACTIONr_angle_other_deg1.0235139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70224.803152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5515556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5121516
X-RAY DIFFRACTIONr_chiral_restr0.0620.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023443
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02645
X-RAY DIFFRACTIONr_mcbond_it0.5941.51868
X-RAY DIFFRACTIONr_mcbond_other0.1471.5739
X-RAY DIFFRACTIONr_mcangle_it1.13522999
X-RAY DIFFRACTIONr_scbond_it1.82331249
X-RAY DIFFRACTIONr_scangle_it2.7934.51218
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
147TIGHT POSITIONAL0.320.05
1467MEDIUM POSITIONAL0.70.5
564LOOSE POSITIONAL1.65
147TIGHT THERMAL0.770.5
1467MEDIUM THERMAL0.752
564LOOSE THERMAL1.0810
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 74 -
Rwork0.389 1305 -
all-1379 -
obs--99.86 %
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)
112.5563-6.98566.01563.8192-4.26457.8458-0.4948-0.956-0.71550.16630.68170.2988-0.2669-0.9354-0.18691.03670.1433-0.06760.31260.04560.166242.11624.05124.697
25.7532-3.8531-1.81496.5805-1.14594.89030.60670.1599-0.0658-0.894-0.2231-0.0727-0.3693-0.1401-0.38360.43690.0080.05320.18160.03380.089257.7611.79437.789
315.9968-11.07192.65877.7067-2.43123.21070.0321-0.4508-0.69230.02980.14660.6124-0.30630.1234-0.17870.28470.0494-0.05730.0858-0.02470.262529.05820.44856.185
46.4283-0.5018-1.96183.01921.20014.0795-0.1604-0.8247-0.48950.06720.0445-0.0913-0.31970.80220.11590.13190.00440.00750.24360.11810.09950.8768.38356.013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 76
2X-RAY DIFFRACTION2A77 - 187
3X-RAY DIFFRACTION3B7 - 73
4X-RAY DIFFRACTION4B74 - 187

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