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- PDB-3egq: Crystal structure of a tetr-family transcriptional regulator (af_... -

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Basic information

Entry
Database: PDB / ID: 3egq
TitleCrystal structure of a tetr-family transcriptional regulator (af_1817) from archaeoglobus fulgidus at 2.55 A resolution
ComponentsTetR family Transcriptional regulator
KeywordsTRANSCRIPTION / Dna-binding / transcription regulation / bacterial regulatory proteins / dna/rna-binding 3-helical bundle fold / helix turn helix motif / hth motif / transcription regulator / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / 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
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Transcriptional regulatory protein, TetR family
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of TetR-family transcriptional regulator (NP_070644.1) from ARCHAEOGLOBUS FULGIDUS at 2.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: 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
Revision 1.5Oct 30, 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_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_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: TetR family Transcriptional regulator
B: TetR family Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7794
Polymers41,0382
Non-polymers7412
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-29 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.550, 61.040, 109.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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
11SERSERLYSLYS3AA5 - 376 - 38
21SERSERLYSLYS3BB5 - 376 - 38
12SERSERGLUGLU4AA38 - 4539 - 46
22SERSERGLUGLU4BB38 - 4539 - 46
13SERSERLEULEU3AA46 - 11847 - 119
23SERSERLEULEU3BB46 - 11847 - 119
14PHEPHEPROPRO4AA119 - 125120 - 126
24PHEPHEPROPRO4BB119 - 125120 - 126
15ARGARGLEULEU3AA126 - 144127 - 145
25ARGARGLEULEU3BB126 - 144127 - 145
16PHEPHEGLUGLU4AA146 - 152147 - 153
26PHEPHEGLUGLU4BB146 - 152147 - 153
17LYSLYSPHEPHE3AA153 - 161154 - 162
27LYSLYSPHEPHE3BB153 - 161154 - 162

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Components

#1: Protein TetR family Transcriptional regulator


Mass: 20519.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: NP_070644.1, AF_1817 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: O28458
#2: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.35
Details: 0.2M sodium chloride, 38.4% polyethylene glycol 200, 0.1M phosphate-citrate pH 4.35, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97927, 0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 1, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979271
30.979131
ReflectionResolution: 2.55→29.412 Å / Num. obs: 13034 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.119 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 13.52
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.54-2.630.3012.739052087185.6
2.63-2.740.2223.749192541198.9
2.74-2.860.1874.444412298198.2
2.86-3.010.1166.447202442198.5
3.01-3.20.0848.847502455199
3.2-3.440.0513.145942361198.9
3.44-3.790.03418.247732472198.3
3.79-4.330.0272346242383197.7
4.33-5.440.0262647012395197.5
5.44-29.4120.02527.846742393194.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.55→29.412 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 26.718 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.713 / ESU R Free: 0.328
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORA DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORA DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE M RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERIN POWER DUE TO PARTIAL S-MET INCORPORATION. 4.TWO PEG 200 FRAGMENT (PE8) FROM MOLECULES FROM THE CRYSTALLIZATION CONDITIONS WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 643 4.9 %RANDOM
Rwork0.243 ---
obs0.244 13001 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.11 Å2 / Biso mean: 58.375 Å2 / Biso min: 32.59 Å2
Baniso -1Baniso -2Baniso -3
1--3.63 Å20 Å20 Å2
2--4.45 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 50 9 2574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222621
X-RAY DIFFRACTIONr_bond_other_d0.0050.021794
X-RAY DIFFRACTIONr_angle_refined_deg2.2621.9823510
X-RAY DIFFRACTIONr_angle_other_deg1.90334381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4885329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.35623.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1215451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5481511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022856
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02538
X-RAY DIFFRACTIONr_nbd_refined0.1350.2569
X-RAY DIFFRACTIONr_nbd_other0.0910.21351
X-RAY DIFFRACTIONr_nbtor_refined0.1220.21238
X-RAY DIFFRACTIONr_nbtor_other0.0630.21066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.10.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.24
X-RAY DIFFRACTIONr_mcbond_it1.79931981
X-RAY DIFFRACTIONr_mcbond_other0.4063662
X-RAY DIFFRACTIONr_mcangle_it2.55152612
X-RAY DIFFRACTIONr_scbond_it6.07381085
X-RAY DIFFRACTIONr_scangle_it7.3211898
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
791TIGHT POSITIONAL0.090.05
272MEDIUM POSITIONAL0.440.5
853LOOSE POSITIONAL0.545
791TIGHT THERMAL0.140.5
272MEDIUM THERMAL0.962
853LOOSE THERMAL2.6610
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 55 -
Rwork0.307 846 -
all-901 -
obs--95.04 %
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)
15.8278-0.21741.63072.2023-0.02572.7533-0.1158-0.45110.6280.4035-0.1299-0.022-0.1711-0.06020.2458-0.0114-0.02040.0162-0.11660.0042-0.08150.910332.160850.6475
21.9878-1.4978-0.57783.39021.67491.81470.01740.38460.14540.0289-0.14040.04540.0509-0.16430.123-0.1296-0.01310.02070.06580.0482-0.132640.311518.906228.9412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 165
2X-RAY DIFFRACTION2B1 - 164

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