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- PDB-3nrv: Crystal structure of MarR/EmrR family transcriptional regulator f... -

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Basic information

Entry
Database: PDB / ID: 3nrv
TitleCrystal structure of MarR/EmrR family transcriptional regulator from Acinetobacter sp. ADP1
ComponentsPutative transcriptional regulator (MarR/EmrR family)
KeywordsTranscription regulator / Transcriptional regulator / PSI-2 / Protein Structure Initiative / Structural Genomics / Midwest Center for Structural Genomics (MCSG)
Function / homology
Function and homology information


DNA-binding transcription factor activity
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
Putative transcriptional regulator (MarR/EmrR family)
Similarity search - Component
Biological speciesAcinetobacter sp. ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsZhang, R. / Wu, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of MarR/EmrR family transcriptional regulator from Acinetobacter sp. ADP1
Authors: Rongguang, Z. / Ruiying, W. / Andrzej, J. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 9, 2020Group: Advisory / Database references / Derived calculations
Category: citation / pdbx_unobs_or_zero_occ_atoms ...citation / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.title / _struct_conn.pdbx_leaving_atom_flag ..._citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 27, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator (MarR/EmrR family)
B: Putative transcriptional regulator (MarR/EmrR family)
C: Putative transcriptional regulator (MarR/EmrR family)
D: Putative transcriptional regulator (MarR/EmrR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,96316
Polymers68,8994
Non-polymers1,06412
Water5,441302
1
A: Putative transcriptional regulator (MarR/EmrR family)
C: Putative transcriptional regulator (MarR/EmrR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1149
Polymers34,4502
Non-polymers6657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-121 kcal/mol
Surface area13090 Å2
MethodPISA
2
B: Putative transcriptional regulator (MarR/EmrR family)
D: Putative transcriptional regulator (MarR/EmrR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8497
Polymers34,4502
Non-polymers3995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-80 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.809, 59.573, 97.753
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative transcriptional regulator (MarR/EmrR family)


Mass: 17224.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. ADP1 (bacteria) / Gene: 2878967, ACIAD1811 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6FBB7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M bis-tris pH 6.5; 2M NH4SO4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jun 26, 2010 / Details: mirrors
RadiationMonochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 56618 / Num. obs: 53697 / % possible obs: 99 % / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 39
Reflection shellResolution: 2→2.03 Å / Redundancy: 5 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.001→32.584 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 23.49 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2295 2856 5.07 %
Rwork0.1957 --
obs0.1975 53697 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.181 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.2554 Å2-0 Å2-0.2274 Å2
2---4.2558 Å20 Å2
3----2.9996 Å2
Refinement stepCycle: LAST / Resolution: 2.001→32.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 60 302 4745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084590
X-RAY DIFFRACTIONf_angle_d1.046148
X-RAY DIFFRACTIONf_dihedral_angle_d17.0651778
X-RAY DIFFRACTIONf_chiral_restr0.079700
X-RAY DIFFRACTIONf_plane_restr0.003771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0013-2.07280.28532610.23265234X-RAY DIFFRACTION98
2.0728-2.15580.25852840.21245302X-RAY DIFFRACTION99
2.1558-2.25390.25343080.21075282X-RAY DIFFRACTION100
2.2539-2.37270.26342920.20885358X-RAY DIFFRACTION99
2.3727-2.52130.25032820.20485322X-RAY DIFFRACTION100
2.5213-2.71580.23212750.20035392X-RAY DIFFRACTION100
2.7158-2.9890.23012620.20255375X-RAY DIFFRACTION100
2.989-3.42110.24453010.19795372X-RAY DIFFRACTION100
3.4211-4.30860.17223090.16535405X-RAY DIFFRACTION100
4.3086-32.58860.22712820.19225472X-RAY DIFFRACTION98
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)
10.85590.08820.5990.9545-0.17390.7639-0.15790.15870.0427-0.22020.08210.1135-0.04580.063400.2035-0.031-0.07640.1820.0210.189226.837229.41978.7363
21.2391-0.3502-0.42091.0511-0.03530.9522-0.157-0.1693-0.05740.20620.1120.16130.0272-0.003200.1990.02170.0760.18470.02060.2-9.689626.31667.8488
30.83580.398-0.14371.3402-0.19661.1498-0.1022-0.02060.036-0.08530.10460.03440.06780.0628-00.19270.03220.00570.1750.00590.161838.40528.751290.2053
40.8062-0.38410.17181.4005-0.06381.2723-0.09630.0449-0.06630.07380.09590.0336-0.05370.0664-00.1751-0.03460.00020.16390.0060.1471.913127.117856.4163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A resid 3:145
2X-RAY DIFFRACTION2chain B resid 2:145
3X-RAY DIFFRACTION3chain C resid 4:145
4X-RAY DIFFRACTION4chain D resid 4:145

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