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- PDB-2nnn: Crystal structure of probable transcriptional regulator from Pseu... -

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Basic information

Entry
Database: PDB / ID: 2nnn
TitleCrystal structure of probable transcriptional regulator from Pseudomonas aeruginosa
ComponentsProbable transcriptional regulator
KeywordsTRANSCRIPTION / Pseudomonas aeruginosa / probable transcriptional regulator / Structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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
Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsChang, C. / Evdokimova, E. / Altamentova, S. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of probable transcriptional regulator from Pseudomonas aeruginosa
Authors: Chang, C. / Evdokimova, E. / Altamentova, S. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transcriptional regulator
B: Probable transcriptional regulator
C: Probable transcriptional regulator
D: Probable transcriptional regulator
E: Probable transcriptional regulator
F: Probable transcriptional regulator
G: Probable transcriptional regulator
H: Probable transcriptional regulator
I: Probable transcriptional regulator
J: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)153,13210
Polymers153,13210
Non-polymers00
Water8,683482
1
A: Probable transcriptional regulator
B: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)30,6262
Polymers30,6262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-28 kcal/mol
Surface area13250 Å2
MethodPISA
2
C: Probable transcriptional regulator
D: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)30,6262
Polymers30,6262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-26 kcal/mol
Surface area13060 Å2
MethodPISA
3
E: Probable transcriptional regulator
F: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)30,6262
Polymers30,6262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-25 kcal/mol
Surface area13270 Å2
MethodPISA
4
G: Probable transcriptional regulator
H: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)30,6262
Polymers30,6262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-25 kcal/mol
Surface area13160 Å2
MethodPISA
5
I: Probable transcriptional regulator
J: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)30,6262
Polymers30,6262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-25 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.373, 89.373, 217.238
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Probable transcriptional regulator


Mass: 15313.190 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1603 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3) derivatives / References: UniProt: Q9I3B8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M Ammonium sulfate, 0.1M Sodium acetate pH4.6, 23% PEG 4000, 0.6M PPS, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97914, 0.97928
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 5, 2006
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979141
20.979281
ReflectionResolution: 2.4→50 Å / Num. all: 75992 / Num. obs: 75944 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.03
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.26 / Num. unique all: 7640 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→34.14 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.969 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26222 3767 5 %RANDOM
Rwork0.21834 ---
all0.22056 71218 --
obs0.22056 71218 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.341 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å21.34 Å20 Å2
2--2.69 Å20 Å2
3----4.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10024 0 0 482 10506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210131
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.99513710
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52351316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37823.148467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.895151755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.21315140
X-RAY DIFFRACTIONr_chiral_restr0.0810.21599
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027712
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.25019
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2880.27102
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5141.56817
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.843210391
X-RAY DIFFRACTIONr_scbond_it1.46933670
X-RAY DIFFRACTIONr_scangle_it2.5054.53319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 278 -
Rwork0.255 5278 -
obs--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)
10.13640.26770.13890.7791-0.58123.0147-0.0629-0.0952-0.04840.036-0.0478-0.0419-0.3781-0.16930.1107-0.1037-0.0503-0.0191-0.0165-0.0484-0.0938-23.878-9.05164.511
20.42951.0834-0.26032.7513-0.81691.54850.0324-0.00580.0553-0.00450.0335-0.08880.4898-0.0698-0.06580.032-0.1071-0.0363-0.0694-0.008-0.1229-31.336-31.53967.786
30.7706-0.2291-0.50840.28470.40363.956-0.0962-0.0034-0.0326-0.0536-0.00390.0048-0.37-0.19960.1001-0.1035-0.0522-0.0531-0.0459-0.007-0.0821-24.906-9.6351.017
43.1492-0.3145-0.1810.03420.10272.59030.02160.1231-0.00220.03230.03560.11990.22280.5309-0.0571-0.159-0.0091-0.0260.1035-0.0358-0.1358-1.697-14.40947.746
51.7521.19250.37470.8438-0.15055.20020.4022-0.29790.30320.1127-0.37250.0857-0.337-0.1206-0.0297-0.105-0.12960.06970.0503-0.1077-0.0914-23.691-2.729106.712
63.00083.758-1.91984.7063-2.40421.22820.5469-0.4798-0.27090.5649-0.6315-0.069-0.07570.57150.0846-0.0143-0.0982-0.07780.06290.0372-0.1251-32.807-24.262112.29
70.84430.3491-0.93430.44560.51043.70370.08590.01810.064-0.0528-0.07870.0789-0.3825-0.0676-0.0072-0.1483-0.05520.00170.056-0.0057-0.1041-25.032-4.67293.303
85.1826-0.06740.06070.3618-0.23560.15350.1248-0.0493-0.07530.04920.0023-0.0670.15190.0162-0.1271-0.1636-0.0169-0.04080.0858-0.0353-0.1427-2.519-11.4890.495
91.1417-0.1274-0.74790.72081.30633.6697-0.2088-0.039-0.0580.19010.2509-0.05330.02180.26-0.04210.1596-0.0648-0.0193-0.1153-0.0195-0.18759.67921.28178.003
101.5024-1.85340.5745.66060.10391.6389-0.46220.04690.14140.19510.57760.24250.0448-0.3703-0.1154-0.0576-0.0107-0.02840.04390.115-0.1584-5.86539.78880.717
110.6258-0.40741.24892.63652.11946.1191-0.2115-0.08320.0188-0.61410.4255-0.0672-0.61740.4885-0.21410.231-0.24050.0566-0.1315-0.0077-0.200510.47222.29264.55
121.44712.5376-0.6094.6418-0.35912.8738-0.24520.1453-0.0011-0.32550.35620.2336-0.1383-0.2932-0.111-0.0416-0.0754-0.0976-0.03510.0695-0.0948-4.9174.52660.755
130.6694-0.2669-0.73640.7734-0.27474.74270.39690.364-0.2708-0.1586-0.37590.02620.3476-0.1874-0.021-0.06840.1727-0.07610.0981-0.1052-0.09420.948-23.10281.221
143.3213-4.21671.91335.4075-2.23171.82380.61170.42130.2953-0.5529-0.7236-0.21830.0180.4810.112-0.0290.10290.0760.03360.0352-0.120611.904-1.56175.684
150.905-0.19451.14860.64751.05674.41880.1212-0.0168-0.04840.0867-0.07120.13140.4587-0.0052-0.05-0.13990.0616-0.0140.0379-0.0014-0.120819.658-21.12394.648
165.3311-0.1561-0.38030.186-0.16140.19110.073-0.06580.0927-0.06280.0502-0.0444-0.09780.0496-0.1232-0.150.01840.04380.0698-0.0226-0.135342.155-14.33997.436
171.575-0.54392.25541.21950.86555.8505-0.0483-0.7228-0.0488-0.08640.18890.0690.0738-0.8974-0.1406-0.26570.01780.01610.39380.0584-0.208820.101-23.7150.96
183.55570.5439-0.67810.1099-0.29221.46150.1736-0.47710.1784-0.1223-0.0317-0.0957-0.42380.0171-0.1419-0.0859-0.0470.02280.059-0.101-0.110243.235-19.27954.78
191.2349-0.19570.63540.4466-0.88863.720.2806-0.0011-0.135-0.1585-0.15060.02010.1654-0.0601-0.13-0.08980.0812-0.01790.1174-0.0036-0.159221.428-23.52937.544
202.3203-2.6160.71993.6720.43162.36270.5102-0.32670.2992-0.5365-0.43850.0023-0.42030.2452-0.07170-0.06320.08220.0049-0.0893-0.142613.157-0.85234.802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 338 - 33
2X-RAY DIFFRACTION1AA107 - 140107 - 140
3X-RAY DIFFRACTION2AA34 - 10634 - 106
4X-RAY DIFFRACTION3BB8 - 338 - 33
5X-RAY DIFFRACTION3BB107 - 140107 - 140
6X-RAY DIFFRACTION4BB34 - 10634 - 106
7X-RAY DIFFRACTION5CC8 - 338 - 33
8X-RAY DIFFRACTION5CC107 - 140107 - 140
9X-RAY DIFFRACTION6CC34 - 10634 - 106
10X-RAY DIFFRACTION7DD8 - 338 - 33
11X-RAY DIFFRACTION7DD107 - 140107 - 140
12X-RAY DIFFRACTION8DD34 - 10634 - 106
13X-RAY DIFFRACTION9EE8 - 338 - 33
14X-RAY DIFFRACTION9EE107 - 140107 - 140
15X-RAY DIFFRACTION10EE34 - 10634 - 106
16X-RAY DIFFRACTION11FF8 - 338 - 33
17X-RAY DIFFRACTION11FF107 - 140107 - 140
18X-RAY DIFFRACTION12FF34 - 10634 - 106
19X-RAY DIFFRACTION13GG8 - 338 - 33
20X-RAY DIFFRACTION13GG107 - 140107 - 140
21X-RAY DIFFRACTION14GG34 - 10634 - 106
22X-RAY DIFFRACTION15HH8 - 338 - 33
23X-RAY DIFFRACTION15HH107 - 140107 - 140
24X-RAY DIFFRACTION16HH34 - 10634 - 106
25X-RAY DIFFRACTION17II8 - 338 - 33
26X-RAY DIFFRACTION17II107 - 140107 - 140
27X-RAY DIFFRACTION18II34 - 10634 - 106
28X-RAY DIFFRACTION19JJ8 - 338 - 33
29X-RAY DIFFRACTION19JJ107 - 140107 - 140
30X-RAY DIFFRACTION20JJ34 - 10634 - 106

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