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- PDB-2f7b: CatM effector binding domain -

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Basic information

Entry
Database: PDB / ID: 2f7b
TitleCatM effector binding domain
ComponentsHTH-type transcriptional regulator catM
KeywordsGENE REGULATION / LTTR / lysR-type transcriptional regulator / inducer binding domain / effector binding domain
Function / homology
Function and homology information


: / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator CatM
Similarity search - Component
Biological speciesAcinetobacter baylyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsClark, T. / Haddad, S. / Ezezika, O. / Neidle, E. / Momany, C.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Distinct Effector-binding Sites Enable Synergistic Transcriptional Activation by BenM, a LysR-type Regulator.
Authors: Ezezika, O.C. / Haddad, S. / Clark, T.J. / Neidle, E.L. / Momany, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of the effector-binding domains of BenM and CatM, LysR-type transcriptional regulators from Acinetobacter sp. ADP1.
Authors: Clark, T. / Haddad, S. / Neidle, E. / Momany, C.
History
DepositionNov 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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

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Assembly

Deposited unit
A: HTH-type transcriptional regulator catM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6326
Polymers26,2131
Non-polymers4205
Water6,467359
1
A: HTH-type transcriptional regulator catM
hetero molecules

A: HTH-type transcriptional regulator catM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,26512
Polymers52,4252
Non-polymers83910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+11
Buried area4170 Å2
ΔGint-134 kcal/mol
Surface area18790 Å2
MethodPISA
2
A: HTH-type transcriptional regulator catM
hetero molecules

A: HTH-type transcriptional regulator catM
hetero molecules

A: HTH-type transcriptional regulator catM
hetero molecules

A: HTH-type transcriptional regulator catM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,52924
Polymers104,8514
Non-polymers1,67920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area11770 Å2
ΔGint-358 kcal/mol
Surface area34910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.184, 75.529, 102.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1004-

SO4

DetailsThe biological unit (effector binding domain) is a dimer generated from the monomer in the asymmetric unit by the operation, 1-x, y, -z

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Components

#1: Protein HTH-type transcriptional regulator catM / Cat operon transcriptional regulator


Mass: 26212.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi (bacteria) / Strain: ADP1 / Gene: catM, catR / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07774
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 288 K / Method: microbatch under oil
Details: PEG 4000, ammonium sulfate, sodium acetate, NaCl, tris, glycerol, imidazole, microbatch under oil, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.00727 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00727 Å / Relative weight: 1
ReflectionResolution: 1.8→60.746 Å / Num. all: 22581 / Num. obs: 22581 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 20.47029 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 29.7
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 88.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 7.5 / Num. measured obs: 2107 / Num. unique all: 2107 / Χ2: 1.44 / % possible all: 88.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2F6G

2f6g


Resolution: 1.9→60.746 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.186 / SU B: 7.879 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: 14 TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.159 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 1007 5.186 %Random
Rwork0.1718 ---
all0.175 18410 --
obs0.175 18410 94.441 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 19.847 Å2
Baniso -1Baniso -2Baniso -3
1-0.296 Å20 Å20 Å2
2--0.682 Å20 Å2
3----0.978 Å2
Refinement stepCycle: LAST / Resolution: 1.9→60.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 21 359 2068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221754
X-RAY DIFFRACTIONr_bond_other_d0.0010.021781
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9942387
X-RAY DIFFRACTIONr_angle_other_deg0.7273.0014067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3915217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54324.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19115314
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg16.097153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.931158
X-RAY DIFFRACTIONr_chiral_restr0.0590.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_nbd_refined0.1830.2311
X-RAY DIFFRACTIONr_nbd_other0.1570.21862
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2801
X-RAY DIFFRACTIONr_nbtor_other0.0770.21074
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.227
X-RAY DIFFRACTIONr_mcbond_it0.77821403
X-RAY DIFFRACTIONr_mcbond_other0.0812432
X-RAY DIFFRACTIONr_mcangle_it1.1751755
X-RAY DIFFRACTIONr_mcangle_other0.49951468
X-RAY DIFFRACTIONr_scbond_it2.3627755
X-RAY DIFFRACTIONr_scbond_other0.7471538
X-RAY DIFFRACTIONr_scangle_it3.16110630
X-RAY DIFFRACTIONr_scangle_other1.312102599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.9-1.9490.278630.20913710.212147197.485
1.949-2.0030.233790.19213590.195147397.624
2.003-2.0610.254690.18613100.189141197.732
2.061-2.1240.293740.17812670.184137797.386
2.124-2.1940.496380.3545010.365134939.956
2.194-2.270.263570.17812140.182129997.844
2.27-2.3560.195600.1811630.181124997.918
2.356-2.4520.215700.17611390.178122898.453
2.452-2.5610.225500.17510930.177115798.79
2.561-2.6860.215660.16910210.172110298.639
2.686-2.8310.258500.1799960.182106098.679
2.831-3.0020.249530.1679570.171101899.214
3.002-3.2090.179520.1628690.16293298.82
3.209-3.4650.211490.1518420.15490099
3.465-3.7940.224490.1467640.1581999.267
3.794-4.240.257350.1397080.14474699.598
4.24-4.8920.204290.1296260.13265999.393
4.892-5.9820.214250.1675490.16957699.653
5.982-8.4190.206220.1894310.1945799.125
8.419-60.7460.318170.2472300.25127789.17
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)
12.9727-0.4633-0.18633.07861.40612.868-0.06110.0458-0.0361-0.0047-0.00380.1243-0.1851-0.09890.065-0.04160.00310.0170.0340.0244-0.048450.79617.88355.696
27.21833.4069-2.065817.3811-4.47338.6557-0.42140.33470.3727-1.01850.4110.2282-0.23760.03040.0105-0.0773-0.0002-0.05960.20670.0190.075640.0917.19950.73
34.8257-0.2011-1.28021.46050.71961.9671-0.0287-0.01610.42740.06060.0315-0.0434-0.32420.002-0.00280.01190.01320.0073-0.03540.0225-0.015352.9627.64461.733
411.80364.43218.04175.5541.4578.6977-0.212-0.2231-0.030.37620.0608-0.2257-0.49740.26750.15120.02060.00830.04580.0204-0.0098-0.025650.89427.06572.291
516.9209-10.5499-6.72546.76834.81214.6831-0.3005-0.2932-0.10590.33190.2356-0.2159-0.28420.1250.06490.0023-0.00420.0360.01530.03450.010255.5713.48769.363
65.9591-1.2712-2.92614.97410.70563.80410.1611-0.1486-0.05470.06510.1045-0.48520.09820.294-0.2656-0.03550.0118-0.06740.0158-0.01770.001178.9377.77362.274
73.09212.82660.759514.75125.87542.9319-0.12130.0659-0.03090.07150.1679-0.3020.01540.3875-0.0466-0.0097-0.0081-0.06870.007-0.0122-0.02878.98.98271.497
817.0563-5.74031.50527.2752-1.76692.357-0.268-0.08770.01410.49520.0736-0.1626-0.39940.06730.19440.0091-0.0708-0.02810.00770.0003-0.080374.58223.06563.186
94.6898-1.99692.69581.0235-2.0726.4807-0.1678-0.29090.28010.19780.0181-0.0855-0.5668-0.02370.14970.0291-0.031-0.06170.0134-0.0460.022672.83722.84371.58
101.38950.38781.23995.2489-0.16641.15740.02040.0570.1087-0.1198-0.0458-0.0946-0.21010.07910.02540.0012-0.01770.00330.0514-0.0016-0.025374.15620.41156.481
116.52272.96292.20723.1940.58182.7306-0.09050.08640.1025-0.15270.14650.01350.13110.104-0.056-0.00760.00020.00110.02890.01710.003170.61912.89660.437
120.4466-0.0589-1.63971.06120.40628.6489-0.1062-0.0096-0.02170.1431-0.1361-0.00080.2055-0.28220.2422-0.0378-0.024-0.00130.0331-0.025-0.00171.7878.93464.237
132.1528-1.57421.82654.4081-0.02562.0766-0.1283-0.3363-0.17730.2095-0.06640.3179-0.159-0.30510.1947-0.05530.04430.07050.08490.0164-0.014744.19420.83764.908
146.2677-0.71684.86563.8434-1.5644.0470.0627-0.28170.19960.4102-0.02510.4071-0.1308-0.4761-0.0375-0.0193-0.00560.05860.02630.01560.048148.8386.23765.78
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1190 - 11210 - 32
22113 - 12033 - 40
33121 - 14841 - 68
44149 - 15669 - 76
55157 - 16377 - 83
66164 - 17584 - 95
77176 - 18896 - 108
88189 - 199109 - 119
99200 - 220120 - 140
1010221 - 237141 - 157
1111238 - 250158 - 170
1212251 - 266171 - 186
1313267 - 289187 - 209
1414290 - 303210 - 223

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