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- PDB-4rgu: Crystal Structure of Putative MarR Family Transcriptional Regulat... -

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Basic information

Entry
Database: PDB / ID: 4rgu
TitleCrystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP complexed with ferulic acid
ComponentsRepressor protein
KeywordsTRANSCRIPTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / winged helix-turn-helix
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
MarR family / 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
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Repressor protein
Similarity search - Component
Biological speciesAcinetobacter sp. ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.891 Å
AuthorsKim, Y. / Joachimiak, G. / Bigelow, L. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2014
Title: Crystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP complexed with ferulic acid
Authors: Kim, Y. / Joachimiak, G. / Bigelow, L. / Cobb, G. / Joachimiak, A.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Nov 27, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Repressor protein
B: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,58411
Polymers36,7332
Non-polymers8519
Water2,990166
1
A: Repressor protein
B: Repressor protein
hetero molecules

A: Repressor protein
B: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,16722
Polymers73,4664
Non-polymers1,70118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area19020 Å2
ΔGint-116 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.668, 82.812, 63.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsto generate tetramer apply x,y,z and -x,-y,z to the asymmetric unit of dimer

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Repressor protein / Repressor protein of the Hydroxycinnamate (Hca) catabolic genes


Mass: 18366.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. ADP1 (bacteria) / Gene: ACIAD1728, hcaR / Plasmid: pMCSG19C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q7X0D9

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Non-polymers , 5 types, 175 molecules

#2: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.4 M Sodium Malonate pH 7.0, 0.1 M Bis-Tris Propane pH 7.0, 5mM ferulic acid, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 17, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.891→50 Å / Num. all: 26574 / Num. obs: 26574 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 32.72 Å2 / Rsym value: 0.063 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1121 / Rsym value: 0.337 / % possible all: 83

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.891→29.509 Å / SU ML: 0.2 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1325 5.05 %random
Rwork0.175 ---
all0.176 26262 --
obs0.176 26262 96.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.9 Å2
Refinement stepCycle: LAST / Resolution: 1.891→29.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 55 166 2464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062461
X-RAY DIFFRACTIONf_angle_d0.9473343
X-RAY DIFFRACTIONf_dihedral_angle_d17.625966
X-RAY DIFFRACTIONf_chiral_restr0.058386
X-RAY DIFFRACTIONf_plane_restr0.004437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8914-1.96720.3741140.32172386250084
1.9672-2.05670.23151400.22642676281694
2.0567-2.16510.22141420.18612750289297
2.1651-2.30070.2881340.23232646278092
2.3007-2.47820.2141720.18442791296399
2.4782-2.72740.24761550.18382855301099
2.7274-3.12170.20761520.18228683020100
3.1217-3.93160.1821520.155229293081100
3.9316-29.51290.17691640.15233036320099
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)
19.94485.41670.10834.99843.03384.43961.001-2.8854-1.74151.91530.29470.40570.3178-0.4892-0.4810.4463-0.08940.0150.65480.19550.40518.3866.703728.3604
20.88310.2216-1.48031.4774-1.59625.94950.0078-0.01170.026-0.1624-0.1713-0.3194-0.29110.49910.19320.3187-0.06580.04680.2668-0.01780.293718.629215.55195.7025
37.65621.0431-3.3299.92160.37642.1860.36010.06010.7136-0.0791-0.52170.9459-1.3438-0.90670.00610.76860.04780.04760.436-0.00190.46528.028127.28192.4482
49.0119-0.3154-5.86822.1270.4443.84360.81220.07321.1080.0502-0.3771-0.3239-1.6321-0.009-0.63090.9488-0.06480.04650.42170.1060.574217.737431.6327-1.9256
55.7955.85250.79229.9946-0.09786.4361-0.03952.36382.2067-1.5587-0.37380.2296-1.0529-1.1050.70320.94550.2545-0.04620.76340.1690.522214.594328.3295-12.5564
62.8254.20852.95668.05413.05564.16040.72731.6917-1.23140.58810.1754-0.9387-0.25930.9706-0.59411.1355-0.31810.06371.9227-0.10891.7543-1.16134.8529-14.362
72.7533-1.27420.97876.8132-6.40449.10150.22720.4684-0.065-0.4501-0.47660.09330.01260.16650.39470.4445-0.04850.05120.3527-0.09190.24915.114513.5373-5.0726
82.3992-1.5374-0.98097.64442.81843.21280.04480.0671-0.0767-0.4209-0.1308-0.01960.1484-0.28490.09250.2813-0.07230.03010.2380.00050.19943.77136.73539.4033
99.58457.89227.68979.55839.38289.2247-1.02082.02122.6298-2.206-0.69471.0918-3.2691.3780.90440.7006-0.1522-0.11050.65040.12220.67181.907625.532815.383
103.3254-0.41522.72545.18991.28163.479-0.22971.1301-1.0209-2.98250.66221.3513-0.0409-0.1607-0.37870.8294-0.1171-0.15530.5165-0.0170.52514.32488.6799-0.8403
112.50271.92372.71285.1825.39368.8157-0.2403-0.03280.3163-0.61630.2634-0.0315-0.91850.06880.03140.2604-0.0550.01490.203-0.01650.24369.350921.205817.2077
126.2711.13321.26455.59-1.04486.5106-0.2077-0.02040.08880.11790.0450.1103-0.24490.44450.17570.1297-0.03320.03520.1972-0.04060.161518.014418.843629.8808
131.5444-0.6227-1.573610.00497.56416.5174-0.20310.8313-1.65630.5402-0.1434-0.82961.75330.57060.48350.35020.23180.01270.75680.07780.614126.33418.298330.7225
142.3974-0.28183.64289.55570.29558.8984-0.53430.8113-0.271-0.61010.3321-0.73560.13541.55960.17980.2193-0.00880.04610.6131-0.09330.322925.309414.389422.385
156.04490.1406-1.29535.77112.32589.2095-0.41220.7015-0.0771-0.66480.3122-0.3524-0.41890.7436-0.01830.2719-0.1192-0.00260.5024-0.03750.282928.464622.667429.6231
166.7293-3.53584.36772.5351-2.743.0588-0.0576-0.4763-0.3650.6833-0.1547-0.3393-0.2684-0.13880.49820.2474-0.0647-0.03830.42580.00360.360825.768518.385639.7371
174.1944.2982-0.32485.69561.72724.555-0.48570.769-1.89692.0232-0.12742.86742.07080.04530.75711.41360.08850.06920.7327-0.12011.847935.45044.344938.6812
188.7421-3.77591.11682.23490.82977.0591-0.0652-0.0724-0.72210.2630.3234-0.64580.1571-0.3322-0.30980.2137-0.06580.04640.3839-0.00670.45626.371112.971838.9488
193.83180.8564.36030.27420.47424.5845-0.2077-0.72770.04860.1735-0.07480.1767-0.0633-0.44410.23370.2315-0.0190.06160.342-0.05280.23357.630517.863531.3915
205.2472-1.296-2.30213.06911.35133.9678-0.1333-0.568-0.3068-0.19110.05330.07170.16560.11870.0590.2439-0.0852-0.02640.1575-0.01060.16726.79594.922517.776
214.71.13840.58490.9434-0.47430.6512-0.7505-0.3106-0.4194-0.1951-0.6490.01230.9573-0.03310.6930.954-0.07620.29263.23920.20640.997126.0638-4.36687.6204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 83 )
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 91 )
6X-RAY DIFFRACTION6chain 'A' and (resid 92 through 98 )
7X-RAY DIFFRACTION7chain 'A' and (resid 99 through 125 )
8X-RAY DIFFRACTION8chain 'A' and (resid 126 through 147 )
9X-RAY DIFFRACTION9chain 'A' and (resid 148 through 153 )
10X-RAY DIFFRACTION10chain 'B' and (resid 11 through 16 )
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 39 )
12X-RAY DIFFRACTION12chain 'B' and (resid 40 through 54 )
13X-RAY DIFFRACTION13chain 'B' and (resid 55 through 59 )
14X-RAY DIFFRACTION14chain 'B' and (resid 60 through 70 )
15X-RAY DIFFRACTION15chain 'B' and (resid 71 through 83 )
16X-RAY DIFFRACTION16chain 'B' and (resid 84 through 91 )
17X-RAY DIFFRACTION17chain 'B' and (resid 92 through 98 )
18X-RAY DIFFRACTION18chain 'B' and (resid 99 through 104 )
19X-RAY DIFFRACTION19chain 'B' and (resid 105 through 125 )
20X-RAY DIFFRACTION20chain 'B' and (resid 126 through 149 )
21X-RAY DIFFRACTION21chain 'B' and (resid 150 through 154 )

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