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- PDB-4gcv: Structure of a Putative transcription factor (PA1374)from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 4gcv
TitleStructure of a Putative transcription factor (PA1374)from Pseudomonas aeruginosa
ComponentsPutative transcription protein
KeywordsTRANSCRIPTION / helex-turn-helex / transcription factor / DNA binding
Function / homology
Function and homology information


Helix-turn-helix, HxlR type / HxlR-like helix-turn-helix / HxlR-type HTH domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / HTH hxlR-type domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsChoe, J. / Kim, H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: The X-ray crystal structure of PA1374 from Pseudomonas aeruginosa, a putative oxidative-stress sensing transcriptional regulator.
Authors: Kim, H. / Choe, J.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Data collection
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcription protein
B: Putative transcription protein
C: Putative transcription protein
D: Putative transcription protein
E: Putative transcription protein
F: Putative transcription protein
G: Putative transcription protein
H: Putative transcription protein
I: Putative transcription protein
J: Putative transcription protein
K: Putative transcription protein
L: Putative transcription protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,96939
Polymers234,23112
Non-polymers1,73827
Water13,872770
1
A: Putative transcription protein
B: Putative transcription protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5489
Polymers39,0392
Non-polymers5097
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-35 kcal/mol
Surface area14840 Å2
MethodPISA
2
C: Putative transcription protein
D: Putative transcription protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3416
Polymers39,0392
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-31 kcal/mol
Surface area13880 Å2
MethodPISA
3
E: Putative transcription protein
F: Putative transcription protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1805
Polymers39,0392
Non-polymers1413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-34 kcal/mol
Surface area14390 Å2
MethodPISA
4
G: Putative transcription protein
H: Putative transcription protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2696
Polymers39,0392
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-32 kcal/mol
Surface area14290 Å2
MethodPISA
5
I: Putative transcription protein
J: Putative transcription protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2696
Polymers39,0392
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-35 kcal/mol
Surface area13930 Å2
MethodPISA
6
K: Putative transcription protein
L: Putative transcription protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3647
Polymers39,0392
Non-polymers3255
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-37 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.897, 74.448, 230.492
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative transcription protein


Mass: 19519.275 Da / Num. of mol.: 12 / Mutation: E106Q, E107Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1374 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I3X0
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1M NaCl, 5.9% PEG3350, 0.1M Phosphate-citrate pH3.6 25% Glycerol, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97959 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.3→29.72 Å / Num. all: 97071 / Num. obs: 96489 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 2.3 Å / % possible all: 99.06

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 18.616 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28695 4824 5 %RANDOM
Rwork0.21399 ---
obs0.21763 91451 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13731 0 103 770 14604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02214068
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.96318988
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14151697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.88121.798712
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.864152402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.17615214
X-RAY DIFFRACTIONr_chiral_restr0.1330.22033
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110818
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8271.58546
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.618213679
X-RAY DIFFRACTIONr_scbond_it3.17435522
X-RAY DIFFRACTIONr_scangle_it5.0734.55309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 376 -
Rwork0.289 6403 -
obs--96.43 %
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)
12.23071.28941.10352.99030.68242.0310.14860.0963-0.32340.2092-0.0502-0.08910.268-0.1061-0.09840.08590.0572-0.02860.1731-0.01960.151960.597-6.9743147.2759
22.66840.74960.17953.4907-0.17551.74760.08840.17490.12640.1767-0.07790.08010.0091-0.0222-0.01050.03030.0556-0.00270.1776-0.03810.087163.70767.7245146.5683
33.7669-0.1503-1.59770.89460.15672.51950.0859-0.33610.1809-0.1123-0.0591-0.1509-0.05850.2144-0.02670.1128-0.02560.00290.2765-0.04370.138340.169719.8509114.3977
42.6594-0.35220.51941.7686-0.22272.04430.0766-0.3068-0.1125-0.1759-0.0356-0.00230.0243-0.0542-0.0410.0893-0.0138-0.00970.28430.02540.132127.317716.1676113.8629
54.30070.0046-1.52821.33440.46471.90460.1457-0.26790.2377-0.0749-0.0632-0.2157-0.01170.2815-0.08260.20760.00560.03310.058-0.00540.144140.164919.6195224.4735
63.6541-0.21860.03092.3322-0.0061.51820.1115-0.1651-0.1112-0.1734-0.09170.06250.0430.0388-0.01980.1690.03640.03340.02070.01770.095826.550515.3757223.4642
71.5605-0.3695-0.08592.49980.63592.061-0.2185-0.02380.03780.16110.2715-0.09130.06660.0306-0.0530.2240.0904-0.0020.1714-0.0060.131437.186554.1768190.8521
81.3992-1.31920.40883.1667-1.34263.0018-0.2041-0.0190.01720.08260.23770.2777-0.1333-0.2312-0.03360.18970.05780.03170.16690.02570.160226.646163.802190.4174
91.50531.27910.95752.78861.06932.68510.17530.0906-0.19630.2696-0.1384-0.0470.198-0.0609-0.03680.2419-0.0518-0.0320.14230.01010.149960.7671-6.370737.6398
102.04460.6576-0.49092.3734-0.29532.09730.1740.11590.04440.2956-0.14140.1029-0.05120.0238-0.03260.2339-0.08820.01550.1455-0.00440.126164.06976.470837.0774
112.6711-0.5586-0.03423.41460.03191.4642-0.1913-0.00550.0183-0.02510.209-0.13440.01880.012-0.01770.0775-0.0798-0.02650.10640.02440.086438.329453.9386300.3271
122.0352-1.46010.36444.126-1.6572.1504-0.1882-0.10430.06480.05950.26680.2801-0.2421-0.1894-0.07860.1063-0.06-0.01750.16360.03040.121227.908563.7155301.4393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 154
2X-RAY DIFFRACTION2B11 - 154
3X-RAY DIFFRACTION3C11 - 154
4X-RAY DIFFRACTION4D11 - 154
5X-RAY DIFFRACTION5E11 - 154
6X-RAY DIFFRACTION6F11 - 154
7X-RAY DIFFRACTION7G11 - 154
8X-RAY DIFFRACTION8H11 - 154
9X-RAY DIFFRACTION9I11 - 154
10X-RAY DIFFRACTION10J11 - 154
11X-RAY DIFFRACTION11K11 - 154
12X-RAY DIFFRACTION12L11 - 154

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