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- PDB-2eth: Crystal structure of a marr-like transcriptional regulator (tm081... -

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Basic information

Entry
Database: PDB / ID: 2eth
TitleCrystal structure of a marr-like transcriptional regulator (tm0816) from thermotoga maritima at 2.50 A resolution
Componentstranscriptional regulator, putative, Mar family
KeywordsTRANSCRIPTION / marr family / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / 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 ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / 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
Transcriptional regulator, putative, Mar family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Transcriptional regulator, putative, MAR family (tm0816) from Thermotoga maritima at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.4Nov 6, 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

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Assembly

Deposited unit
A: transcriptional regulator, putative, Mar family
B: transcriptional regulator, putative, Mar family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4313
Polymers36,3962
Non-polymers351
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-66 kcal/mol
Surface area15080 Å2
MethodPISA
2
A: transcriptional regulator, putative, Mar family
B: transcriptional regulator, putative, Mar family
hetero molecules

A: transcriptional regulator, putative, Mar family
B: transcriptional regulator, putative, Mar family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8626
Polymers72,7914
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11860 Å2
ΔGint-115 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.852, 58.439, 80.432
Angle α, β, γ (deg.)90.000, 125.910, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPHEPHE5AA2 - 1714 - 29
21ASPASPPHEPHE5BB2 - 1714 - 29
12LYSLYSGLUGLU5AA31 - 5443 - 66
22LYSLYSGLUGLU5BB31 - 5443 - 66
13PHEPHEVALVAL1AA55 - 6367 - 75
23PHEPHEVALVAL1BB55 - 6367 - 75
14THRTHRARGARG5AA64 - 7876 - 90
24THRTHRARGARG5BB64 - 7876 - 90
15VALVALGLUGLU5AA91 - 140103 - 152
25VALVALGLUGLU5BB91 - 140103 - 152

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein transcriptional regulator, putative, Mar family


Mass: 18197.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm0816 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZS3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.65 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 2.0M (NH4)2SO4, 0.2M NaCl, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 25, 2005
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
ReflectionResolution: 2.3→47.19 Å / Num. obs: 14519 / % possible obs: 87.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.3-2.3645.13.10.6371.25470.637
2.36-2.4253.43.30.5631.36290.563
2.42-2.4964.93.40.5131.57490.513
2.49-2.5776.73.40.4010.78560.401
2.57-2.6696.63.60.3262.210640.326
2.66-2.7598.23.60.2912.510500.291
2.75-2.8597.93.60.2133.49940.213
2.85-2.9798.23.60.1734.29610.173
2.97-3.198.23.60.1275.79230.127
3.1-3.2598.43.60.1016.68930.101
3.25-3.4398.53.60.0818.28400.081
3.43-3.6498.43.60.05711.18030.057
3.64-3.8998.93.60.04613.77550.046
3.89-4.298.43.60.039167090.039
4.2-4.698.93.60.03318.56410.033
4.6-5.1498.93.60.03120.55930.031
5.14-5.9498.83.60.03815.55300.038
5.94-7.27993.50.03516.94480.035
7.27-10.2999.23.50.02520.63430.025
10.29-47.1995.43.30.02127.61910.021

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→45.03 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.641 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.258
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THE NOMINAL RESOLUTION IS 2.50 A WITH 1303 OBSERVED REFLECTIONS BETWEEN 2.50-2.30 (35.8% COMPLETE FOR THIS SHELL) INCLUDED IN THE ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THE NOMINAL RESOLUTION IS 2.50 A WITH 1303 OBSERVED REFLECTIONS BETWEEN 2.50-2.30 (35.8% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT. (3) DISORDERED REGIONS, INCLUDING B19-B24 AND B55-63, WERE DIFFICULT TO MODEL. NCS WAS USED TO MODEL THESE REGIONS. (4) UNKNOWN DENSITIES NEAR A131 AND B58 COULD NOT BE MODELED. (5) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 732 5 %RANDOM
Rwork0.227 ---
all0.229 ---
obs-13786 87.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.957 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20.29 Å2
2---0.03 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 1 47 2190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222181
X-RAY DIFFRACTIONr_bond_other_d0.0010.021456
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9742946
X-RAY DIFFRACTIONr_angle_other_deg0.97533556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28323.45781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12615378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6671511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
X-RAY DIFFRACTIONr_nbd_refined0.2360.2528
X-RAY DIFFRACTIONr_nbd_other0.1920.21437
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21139
X-RAY DIFFRACTIONr_nbtor_other0.0930.21170
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.27
X-RAY DIFFRACTIONr_mcbond_it0.9291.51448
X-RAY DIFFRACTIONr_mcbond_other0.1981.5567
X-RAY DIFFRACTIONr_mcangle_it1.50722259
X-RAY DIFFRACTIONr_scbond_it2.2563823
X-RAY DIFFRACTIONr_scangle_it3.4964.5686
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
196MEDIUM POSITIONAL0.170.5
1100LOOSE POSITIONAL0.565
196MEDIUM THERMAL0.562
1100LOOSE THERMAL1.0510
2142MEDIUM POSITIONAL0.140.5
2177LOOSE POSITIONAL0.325
2142MEDIUM THERMAL1.122
2177LOOSE THERMAL1.8610
396TIGHT POSITIONAL0.040.05
396TIGHT THERMAL0.580.5
489MEDIUM POSITIONAL0.150.5
499LOOSE POSITIONAL0.565
489MEDIUM THERMAL1.282
499LOOSE THERMAL2.3410
5295MEDIUM POSITIONAL0.240.5
5326LOOSE POSITIONAL0.415
5295MEDIUM THERMAL1.292
5326LOOSE THERMAL2.0610
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 19 -
Rwork0.248 527 -
obs--44.86 %
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)
17.9811-4.54786.80384.5122-3.052113.6875-0.07521.1422-0.0325-0.3583-0.0440.2782-0.83481.07150.11910.0034-0.24560.05250.4233-0.1590.09719.825411.36338.108
20.6223-0.4964-0.99751.28530.63164.9359-0.1222-0.13920.08260.11610.04990.1373-0.0804-0.23320.0723-0.1937-0.03890-0.0943-0.0433-0.131218.196919.240224.9892
313.0976-5.43471.176214.6885-4.081310.88190.0250.70930.7019-1.01840.17630.4512-0.117-1.0201-0.2013-0.0388-0.1467-0.03310.06130.0654-0.167419.273321.961416.6476
43.45591.6504-1.38811.0243-0.43740.77290.050.00730.2219-0.00650.06860.3270.1437-0.1276-0.1186-0.0233-0.0709-0.03050.00080.07690.04911.596611.653411.3381
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 2312 - 35
22AA24 - 14036 - 152
33BB0 - 2312 - 35
44BB24 - 14036 - 152

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