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- PDB-7el2: Crystal structure of apo-HpaR from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 7el2
TitleCrystal structure of apo-HpaR from Acinetobacter baumannii
ComponentsHomoprotocatechuate degradation operon regulator HpaR
KeywordsDNA BINDING PROTEIN / MarR family of transcription regulators / Transcription factor in HPA-degradation pathway / Acinetobacter baumannii
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
HTH-type transcriptional regulator HpaR/FarR / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Homoprotocatechuate degradation operon regulator HpaR
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPermsirivisarn, P. / Pakotiprapha, D.
Funding support Thailand, 2items
OrganizationGrant numberCountry
The Thailand Research Fund (TRF)RSA6280087 Thailand
The Thailand Research Fund (TRF)RTA5980001 Thailand
CitationJournal: Febs J. / Year: 2022
Title: Mechanism of transcription regulation by Acinetobacter baumannii HpaR in the catabolism of p-hydroxyphenylacetate.
Authors: Permsirivisarn, P. / Yuenyao, A. / Pramanpol, N. / Charoenwattanasatien, R. / Suginta, W. / Chaiyen, P. / Pakotiprapha, D.
History
DepositionApr 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homoprotocatechuate degradation operon regulator HpaR
B: Homoprotocatechuate degradation operon regulator HpaR


Theoretical massNumber of molelcules
Total (without water)33,0092
Polymers33,0092
Non-polymers00
Water1,02757
1
A: Homoprotocatechuate degradation operon regulator HpaR

B: Homoprotocatechuate degradation operon regulator HpaR


Theoretical massNumber of molelcules
Total (without water)33,0092
Polymers33,0092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area3830 Å2
ΔGint-39 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.069, 78.932, 86.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Homoprotocatechuate degradation operon regulator HpaR


Mass: 16504.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: hpaR, EWO92_01730, EWO96_02085, EWP49_02085, FD887_17210
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Q4GPX4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM sodium acetate, 150 mM CaCl2 and 20% (w/v) PEG6000)
PH range: 5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.2→28.69 Å / Num. obs: 15795 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 41.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.7 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1323 / CC1/2: 0.938 / Rpim(I) all: 0.232 / Rrim(I) all: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2-3472refinement
Blu-Icedata collection
DIALSdata reduction
PHASERphasing
BUCCANEERmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AIQ

5aiq


Resolution: 2.2→28.69 Å / SU ML: 0.3307 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 32.0271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2467 1461 4.99 %
Rwork0.2294 27810 -
obs0.2303 15739 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 0 57 2120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652084
X-RAY DIFFRACTIONf_angle_d1.04612793
X-RAY DIFFRACTIONf_chiral_restr0.06326
X-RAY DIFFRACTIONf_plane_restr0.0063349
X-RAY DIFFRACTIONf_dihedral_angle_d22.9546828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.39731520.33462752X-RAY DIFFRACTION99.97
2.28-2.370.28871550.30812777X-RAY DIFFRACTION99.83
2.37-2.480.36221430.28222771X-RAY DIFFRACTION99.52
2.48-2.610.28331310.27562835X-RAY DIFFRACTION99.9
2.61-2.770.29681600.25892763X-RAY DIFFRACTION99.83
2.77-2.990.26051290.27052802X-RAY DIFFRACTION99.97
2.99-3.290.29191560.25022803X-RAY DIFFRACTION99.93
3.29-3.760.23041390.222810X-RAY DIFFRACTION99.9
3.76-4.730.18671610.18212762X-RAY DIFFRACTION99.97
4.73-28.690.21931350.20632735X-RAY DIFFRACTION97.39
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)
14.094594680031.31565987161-0.01060286084544.00520155455-0.1241885213330.381415836927-0.3714287896950.4249191794040.1519334970090.2267115300610.4672260881870.0830135571326-0.264971322177-0.224927659484-0.1957654326140.727187177048-0.0176158940661-0.01688682436680.469417332590.05448710345950.36897981745-4.6379884076614.3397874808-15.8970646913
25.868433267850.467057377933-1.517680394638.73442247435-0.7589769406128.68449964217-0.169324275284-0.156690173211-0.04199547874580.3386356213290.186312066474-0.4852818812040.4112493589090.756607140311-0.0296327623110.3765705064520.07674152385460.0222817529420.367788796259-0.01255357355070.330329926216-1.77749566989-5.63423417151-6.3609341579
31.550280054372.96212578976-0.8269637867377.75565164223-6.437254860339.74965587749-0.2203790333760.169708501453-0.0937193559975-0.4188365526670.6772420598160.08514486965210.651850808338-1.04460370538-0.6528738453690.450075312447-0.0482250755567-0.01992146387460.4992921302230.01800673052640.456740427969-15.26414504990.545993246592-17.0991228129
48.238001191942.66653744684.130341207816.788719969092.627253338579.112128202970.598593071920.18943430278-0.8318981667240.274596614431-0.373526837527-0.626760093663-0.9418680084050.202598030766-0.1678937863310.558765825112-0.133650919114-0.004375027382410.3484617975240.04600002811850.420210394343-1.863901309746.47385723167-29.9316893524
53.07199341157-2.431820952620.546029011137.06965624015-2.026823479151.11327616066-0.34015853816-0.0352879331572-0.437112835635-0.3873752816440.3231563700960.7765335818230.292416365333-0.06695619435110.06274632684550.5852600957070.0552285377866-0.04103084067030.517873113182-0.0003912769234320.44338429019-9.13024610485-22.0388874474-28.782544371
63.80012368396-0.230003555648-1.18163959384.01453410226-1.222155694964.43538377436-0.314133739930.2933250561310.0186522823995-1.038458880410.379650873208-0.4063770044980.3438147082750.759421851612-0.1628934564860.778295453080.0606288878425-0.03717526340410.547620566949-0.06584618702830.527333606713-2.0972626796-11.6953448627-37.6139027127
78.004517029814.420040173953.072258356764.40949221521.01885853978.06943860458-0.5624024528570.551546269383-0.0961592997004-1.350484464120.642502171709-0.137765336756-0.2877408623450.528422977065-0.04367487475420.6030945940540.00846712918521-0.0246254580230.417009826022-0.0813003808890.405009037999-5.76765201586-1.83200358874-38.6237123752
81.72872658133-1.370785678040.2647680652793.92013633281-5.127505926119.25441685284-0.56168946622-0.203279617656-0.05989901251650.6198535601710.4230736746090.2773076442870.0527507747853-0.4246140718690.01532087113060.5649582938210.117254249441-0.0203723513620.576406841110.06062535586290.590467677046-16.7787599313-16.9713211808-22.2072029405
98.58931995570.968335205285-1.648190362876.23253245440.01892390303126.550333904820.21911179215-0.7388969756380.5737639587610.402842793508-0.1646917705950.103961425484-2.15558324359-0.230438839511-0.09229634982361.089395103770.2501337444490.04901896211710.460386512940.0579451032220.490998797920.123921635409-22.9237054322-13.5445009076
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 30 )AA3 - 301 - 28
22chain 'A' and (resid 31 through 95 )AA31 - 9529 - 85
33chain 'A' and (resid 96 through 120 )AA96 - 12086 - 110
44chain 'A' and (resid 121 through 136 )AA121 - 136111 - 126
55chain 'B' and (resid 7 through 46 )BB7 - 461 - 40
66chain 'B' and (resid 47 through 74 )BB47 - 7441 - 68
77chain 'B' and (resid 75 through 95 )BB75 - 9569 - 85
88chain 'B' and (resid 96 through 120 )BB96 - 12086 - 110
99chain 'B' and (resid 121 through 138 )BB121 - 138111 - 128

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