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- PDB-2hr3: Crystal structure of putative transcriptional regulator protein f... -

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Basic information

Entry
Database: PDB / ID: 2hr3
TitleCrystal structure of putative transcriptional regulator protein from Pseudomonas aeruginosa PA01 at 2.4 A resolution
ComponentsProbable transcriptional regulator
KeywordsTRANSCRIPTION / MCSG / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
: / Helix Hairpins - #100 / MarR family / Immunoglobulin FC, subunit C / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins ...: / Helix Hairpins - #100 / MarR family / Immunoglobulin FC, subunit C / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 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
AuthorsKirillova, O. / Chruszcz, M. / Evdokimova, E. / Kudritska, M. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative transcriptional regulator protein from Pseudomonas aeruginosa PA01 at 2.4 A resolution
Authors: Kirillova, O. / Chruszcz, M. / Evdokimova, E. / Kudritska, M. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionJul 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 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: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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


Theoretical massNumber of molelcules
Total (without water)66,1614
Polymers66,1614
Non-polymers00
Water1,04558
1
A: Probable transcriptional regulator
B: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)33,0812
Polymers33,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-44 kcal/mol
Surface area13100 Å2
MethodPISA
2
C: Probable transcriptional regulator
D: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)33,0812
Polymers33,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-46 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.251, 72.281, 70.043
Angle α, β, γ (deg.)90.00, 101.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12C
22D
32C
42D

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROALAALAAA2 - 842 - 84
211THRTHRHISHISBB3 - 833 - 83
321ARGARGGLUGLUAA91 - 14691 - 146
421THRTHRGLUGLUBB92 - 14592 - 145
112THRTHRASPASPCC3 - 853 - 85
212PROPROPROPRODD2 - 862 - 86
322ARGARGGLUGLUCC91 - 14591 - 145
422ARGARGGLUGLUDD91 - 14591 - 145

NCS ensembles :
ID
1
2
DetailsThe biological assembly is a dimer

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Components

#1: Protein
Probable transcriptional regulator / Putative transcriptional regulator


Mass: 16540.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3067 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q9HZE1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.3 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 296.2 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M di-Ammonium hydrogen citrate, 20% PEG 3350, 500mM Sodium chloride, 10mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97954, 0.97970
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 16, 2006
RadiationMonochromator: Si III CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.97971
ReflectionResolution: 2.4→68.68 Å / Num. all: 23086 / Num. obs: 22942 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 31.3
Reflection shellResolution: 2.4→2.42 Å / Redundancy: 7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 21.597 / SU ML: 0.241 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.457 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28021 1179 5.1 %RANDOM
Rwork0.20813 ---
all0.21191 23086 --
obs0.21191 21763 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.554 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0.57 Å2
2--1.05 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 0 58 4142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0214131
X-RAY DIFFRACTIONr_bond_other_d0.0020.024014
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9775589
X-RAY DIFFRACTIONr_angle_other_deg0.96739124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5875546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59721.552174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.19915684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2341560
X-RAY DIFFRACTIONr_chiral_restr0.1060.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02870
X-RAY DIFFRACTIONr_nbd_refined0.2260.21028
X-RAY DIFFRACTIONr_nbd_other0.1960.23946
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21983
X-RAY DIFFRACTIONr_nbtor_other0.0950.22656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1671.52824
X-RAY DIFFRACTIONr_mcbond_other0.2281.51130
X-RAY DIFFRACTIONr_mcangle_it1.67924296
X-RAY DIFFRACTIONr_scbond_it2.40231443
X-RAY DIFFRACTIONr_scangle_it3.7934.51292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1891loose positional0.715
2C1967loose positional0.725
1A1891loose thermal3.3910
2C1967loose thermal2.9410
LS refinement shellResolution: 2.4→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 79 -
Rwork0.245 1544 -
obs--97.19 %
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)
15.8541-4.3107-0.5463.22640.04352.51430.35770.2061-0.1003-0.1086-0.1404-0.2748-0.00170.1421-0.2174-0.1762-0.03250.0137-0.325-0.00630.117431.842-0.75530.7
21.722-0.9047-1.23320.91590.40183.7123-0.07260.21130.20160.2018-0.2727-0.0417-0.06780.69030.3453-0.2416-0.00160.00890.02520.12210.221327.993.13822.923
31.7615-0.42751.0661.78221.42142.5537-0.2181-0.43680.0160.0678-0.18660.30730.0095-0.79740.4047-0.19670.0067-0.01880.1152-0.06040.137248.7257.38569.047
44.35491.69241.44532.7133-0.99632.4690.2617-0.7453-0.15020.12810.05070.38630.1048-0.316-0.3124-0.2194-0.01310.0508-0.03640.02010.060945.7670.02662.247
55.0789-3.1268-1.26422.59311.71381.6244-0.0227-0.41790.3010.27850.3147-0.45880.13820.2479-0.292-0.09910.0279-0.0001-0.23880.00570.105326.0134.85541.103
63.3007-1.0386-1.67140.33470.32685.83990.15390.6269-0.08550.0985-0.2714-0.0159-0.149-0.26520.1174-0.1110.02460.0388-0.1240.03430.036414.6013.42125.904
73.0135-0.073-0.27660.96070.08965.7924-0.0169-0.47080.06850.0212-0.1046-0.0472-0.04290.27920.1215-0.2421-0.03490.0163-0.1521-0.0024-0.034261.5624.79465.796
88.03411.25120.81962.1574-1.2452.22950.03110.64520.361-0.04280.06230.43390.049-0.1185-0.0934-0.26020.00670.0103-0.1323-0.0123-0.024149.7056.2851.369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 842 - 84
2X-RAY DIFFRACTION2BB3 - 833 - 83
3X-RAY DIFFRACTION3CC3 - 853 - 85
4X-RAY DIFFRACTION4DD2 - 862 - 86
5X-RAY DIFFRACTION5AA91 - 14691 - 146
6X-RAY DIFFRACTION6BB92 - 14592 - 145
7X-RAY DIFFRACTION7CC91 - 14591 - 145
8X-RAY DIFFRACTION8DD91 - 14591 - 145

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