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- PDB-3gzi: CRYSTAL STRUCTURE OF a transcriptional regulator of the tetR fami... -

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Basic information

Entry
Database: PDB / ID: 3gzi
TitleCRYSTAL STRUCTURE OF a transcriptional regulator of the tetR family (SHEW_3567) FROM SHEWANELLA LOIHICA PV-4 AT 2.05 A RESOLUTION
ComponentsTranscriptional regulator, TetR family
KeywordsTRANSCRIPTION / TETR FAMILY TRANSCRIPTIONAL 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
Unknown ligand / Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesShewanella loihica PV-4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of TETR family transcriptional regulator (YP_001095692.1) from SHEWANELLA SP. PV-4 at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,89311
Polymers25,3341
Non-polymers55910
Water2,306128
1
A: Transcriptional regulator, TetR family
hetero molecules

A: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,78522
Polymers50,6682
Non-polymers1,11720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area8310 Å2
ΔGint-3 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.830, 45.836, 68.694
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Transcriptional regulator, TetR family


Mass: 25333.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica PV-4 (bacteria) / Gene: Shew_3567, YP_001095692.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3QIY5
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40.0000% Ethylene-Glycol, 5.0000% PEG-3000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 9, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.05→29.67 Å / Num. obs: 16032 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.881 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.05-2.14.90.7651.8571411760.765100
2.1-2.164.90.5952.3542811180.595100
2.16-2.224.80.4433534011060.443100
2.22-2.294.80.3793.7521110790.379100
2.29-2.374.80.3064.5501210340.306100
2.37-2.454.90.2455.648249940.245100
2.45-2.544.90.2136.547709830.213100
2.54-2.654.80.1757.945269370.175100
2.65-2.764.80.1589.143489010.158100
2.76-2.94.80.13310.541718680.133100
2.9-3.064.80.11112.540118350.111100
3.06-3.244.80.09814.437637830.098100
3.24-3.474.80.08916.435457410.089100
3.47-3.744.80.07818.433026920.078100
3.74-4.14.70.06419.730626460.064100
4.1-4.584.70.0621.127565910.06100
4.58-5.294.60.0672223735160.067100
5.29-6.484.40.07722.519884530.077100
6.48-9.174.20.05523.915533660.055100
9.17-29.673.80.04923.28032130.04997

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→29.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.202 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.18
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE MODEL SHOWS TWO RAMACHANDAN OUTLIERS, ARG 32 AND PRO 33. THESE OUTLIERS ARE SITUATED IN A REGION OF DISORDERED ELECTRON DENSITY BETWEEN RESIDUES 32-38. 5. THERE IS UNIDENTIFIED DENSITY FOUND NEAR THE LIGAND BINDING SITE. IT WAS MODELED AS AN UNKNOWN LIGAND (UNL).
RfactorNum. reflection% reflectionSelection details
Rfree0.248 799 5 %RANDOM
Rwork0.187 ---
obs0.19 16004 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.08 Å2 / Biso mean: 38.319 Å2 / Biso min: 19.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.72 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 44 128 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221741
X-RAY DIFFRACTIONr_bond_other_d0.0090.021220
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9852352
X-RAY DIFFRACTIONr_angle_other_deg1.10132970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78723.5978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82815302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4221514
X-RAY DIFFRACTIONr_chiral_restr0.090.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021943
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02355
X-RAY DIFFRACTIONr_nbd_refined0.2380.2379
X-RAY DIFFRACTIONr_nbd_other0.180.21207
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2866
X-RAY DIFFRACTIONr_nbtor_other0.0870.2858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.218
X-RAY DIFFRACTIONr_mcbond_it2.37331204
X-RAY DIFFRACTIONr_mcbond_other0.4673420
X-RAY DIFFRACTIONr_mcangle_it3.23861739
X-RAY DIFFRACTIONr_scbond_it5.4078712
X-RAY DIFFRACTIONr_scangle_it6.88511613
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 62 -
Rwork0.245 1112 -
all-1174 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 8.9202 Å / Origin y: -15.0819 Å / Origin z: 75.0405 Å
111213212223313233
T-0.0648 Å20.0123 Å2-0.0308 Å2--0.1091 Å2-0.0229 Å2---0.0486 Å2
L1.1459 °20.3079 °2-0.5228 °2-0.4375 °2-0.2547 °2--0.7833 °2
S-0.0336 Å °-0.052 Å °0.0765 Å °0.0195 Å °0.0188 Å °0.0123 Å °0.0025 Å °-0.0517 Å °0.0148 Å °

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