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- PDB-3cnv: Crystal structure of the ligand-binding domain of a putative GntR... -

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Basic information

Entry
Database: PDB / ID: 3cnv
TitleCrystal structure of the ligand-binding domain of a putative GntR-family transcriptional regulator from Bordetella bronchiseptica
ComponentsPutative GntR-family transcriptional regulator
KeywordsTRANSCRIPTION REGULATOR / STRUCTURAL GENOMICS / GNTR / TRANSCRIPTIONAL REGULATOR / BORDETELLA BRONCHISEPTICA / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
UTRA / UbiC transcription regulator-associated / UTRA domain / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family ...UTRA / UbiC transcription regulator-associated / UTRA domain / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Putative GntR-family transcriptional regulator / Putative GntR-family transcriptional regulator
Similarity search - Component
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZimmerman, M.D. / Xu, X. / Cui, H. / Filippova, E.V. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of the ligand-binding domain of a putative GntR-family transcriptional regulator from Bordetella bronchiseptica.
Authors: Zimmerman, M.D. / Xu, X. / Cui, H. / Filippova, E.V. / Savchenko, A. / Edwards, A.M. / Minor, W.
History
DepositionMar 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 5, 2011Group: Structure summary
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Putative GntR-family transcriptional regulator
B: Putative GntR-family transcriptional regulator
C: Putative GntR-family transcriptional regulator
D: Putative GntR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,46513
Polymers74,5314
Non-polymers9349
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-5.7 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.196, 58.071, 65.580
Angle α, β, γ (deg.)82.36, 86.52, 68.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative GntR-family transcriptional regulator


Mass: 18632.752 Da / Num. of mol.: 4 / Fragment: Please see information provided in remark 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Species: Bordetella bronchiseptica / Strain: RB50 / NCTC 13252 / Gene: BB3683 / Plasmid: p15Tv LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q7WD95, UniProt: A0A0H3LYW6*PLUS
#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE COMPLETE SEQUENCE OF THE PURIFIED POLYPEPTIDE IS: (MSE) ...AUTHORS STATE THAT THE COMPLETE SEQUENCE OF THE PURIFIED POLYPEPTIDE IS: (MSE)GSSHHHHHHSSGRENLYFQG(MSE)AEARPDSLTRSRAAKPAGEGAAFSPLY RQIKELLVQSLDRGEWKPGELIPSEIDLAARFQVSQGTVRKAVDELAAEHLLLRRQG KGTFVATHHEARVRYRFLRLAPDEEGEGGRAESRILECRRLRAPAEIARALELRAGE TVVTIRRQLS(MSE)NH(MSE)PTVIDDLWLPGTHFRGLTLELLTASKAPLYGLFES EFGVS(MSE)VRADEKLRAVAASPEIAPLLGVEPGRPLLQVDRISYTYGDRP(MSE) EVRRGLYLTDHYHYRNSLN FROM WHICH (MSE)GSSHHHHHHSSGRENLYFQG IS AN EXPRESSION TAG, AND THE FOLLOWING SEQUENCE MATCHES THE SEQUENCE OF THE UNIPROT ENTRY Q7WD95. AUTHORS ALSO STATE THAT THE CRYSTALLIZATION SOLUTION WAS TREATED WITH A 1:40 DILUTION OF TRYPSIN, WHICH EVIDENTLY CLEAVED OFF MANY OF N-TERMINAL RESIDUES OF THE PROTEIN PRIOR TO CRYSTAL FORMATION. THE PRECISE LOCATION OF THE CLEAVAGE SITE HAS NOT BEEN DETERMINED. THEREFORE, THE SEQUENCE INFORMATION, AS WELL AS THE VALUES OF MATTHEWS COEFFICIENT AND SOLVENT CONTENT ARE BASED ON THE CHAIN LENGTH STARTING FROM THE FIRST VISIBLE N-TERMINAL RESIDUE IN ELECTRON DENSITY.

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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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-tris pH 7.0, 1M Tri-ammonium citrate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorType: APS-1 / Detector: CCD / Date: Feb 23, 2008 / Details: Mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 52604 / Num. obs: 52604 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 18.387
Reflection shellResolution: 2→2.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3 / Rsym value: 0.382 / % possible all: 95.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-2000data reduction
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
ARP/wARPmodel building
REFMAC5.4.0069refinement
HKL-3000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.91 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.137 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2614 5.1 %RANDOM
Rwork0.164 ---
all0.167 51591 --
obs0.167 51591 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20.56 Å2-0.84 Å2
2---1.91 Å20.53 Å2
3---0.26 Å2
Refine analyzeLuzzati coordinate error obs: 0.322 Å
Refinement stepCycle: LAST / Resolution: 2→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 57 395 5451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225185
X-RAY DIFFRACTIONr_bond_other_d0.0010.023671
X-RAY DIFFRACTIONr_angle_refined_deg1.9222.0017045
X-RAY DIFFRACTIONr_angle_other_deg1.4438788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0125637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.95520.342234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76715853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2431581
X-RAY DIFFRACTIONr_chiral_restr0.1130.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215761
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021160
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1621.53190
X-RAY DIFFRACTIONr_mcbond_other0.3391.51277
X-RAY DIFFRACTIONr_mcangle_it2.10225125
X-RAY DIFFRACTIONr_scbond_it3.36731995
X-RAY DIFFRACTIONr_scangle_it5.4044.51915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 187 -
Rwork0.17 3548 -
obs--95.82 %
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)
11.5346-1.03540.48521.421-0.44010.41170.12760.02670.1227-0.14760.0237-0.2293-0.07620.2842-0.1514-0.04260.02320.03740.0628-0.032-0.004965.38827.58140.515
25.13470.9209-0.86043.5449-1.30224.3066-0.0410.0436-0.2915-0.24110.0438-0.05180.4108-0.3177-0.0027-0.07050.0246-0.02270.0269-0.0208-0.070252.64116.11635.866
34.0836-1.18560.6621.58170.79151.81410.02660.01240.1301-0.1773-0.05230.1014-0.0421-0.31280.0257-0.0930.026-0.00550.0636-0.0035-0.059852.69923.51940.239
41.3267-1.02312.33623.14490.16956.75180.29380.3118-0.1587-0.2277-0.05080.13810.50010.265-0.243-0.00120.075-0.02420.111-0.071-0.044369.44911.41931.273
53.346-0.08942.18541.81930.23941.47610.0453-0.1696-0.02450.00390.00860.01590.0206-0.1068-0.0538-0.09310.03060.00540.0557-0.0038-0.058762.52719.30545.008
60.2091-0.44-0.1261.5188-0.26971.6289-0.0599-0.06140.04830.00940.02690.02640.2608-0.09520.033-0.03670.018-0.0032-0.0102-0.02370.010278.5126.72355.882
73.20132.06330.22135.6530.92952.81580.06570.03660.0769-0.1452-0.0151-0.13720.00960.2085-0.0506-0.13480.07540.01090.0071-0.0145-0.021989.74714.25652.98
82.1544-0.60561.47761.278-0.02023.25860.12410.1279-0.0325-0.032-0.0975-0.09230.21960.1516-0.0266-0.1110.0390.0145-0.0116-0.0308-0.008184.00310.95253.654
97.0449-2.1453-0.63499.15462.298510.8868-0.1305-0.20430.44670.34220.0249-0.1213-0.43980.21180.1056-0.13710.0089-0.0157-0.0126-0.02590.025183.51722.11758.223
103.5967-1.0163-0.43771.2215-0.45631.4295-0.03090.0295-0.29370.01810.07070.08560.2275-0.0497-0.0398-0.05630.0343-0.03220.0182-0.0299-0.003770.469.90848.973
110.9769-0.4398-0.0010.4388-0.71022.2128-0.07840.0961-0.0403-0.1816-0.00430.15680.1464-0.32360.0827-0.08810.02230.00990.0475-0.03370.022155.64136.96256.418
129.8088-0.60781.41618.3848-0.40314.1814-0.1746-0.39490.07510.25720.1656-0.5814-0.25620.2630.009-0.0951-0.0280.0027-0.0213-0.04650.015376.86348.36760.174
132.7304-0.7829-0.65541.6931-0.0353.0269-0.01310.05180.20390.02620.0562-0.1609-0.1673-0.1096-0.0431-0.06930.062-0.0057-0.0568-0.02150.010264.40547.21756.9
140.8169-0.3121-0.01612.365-1.28762.3251-0.084-0.01710.15910.20360.1024-0.0635-0.2388-0.181-0.0184-0.07340.0359-0.003-0.0244-0.0351-0.021261.83640.94560.684
151.32060.86480.65092.7989-0.19571.1328-0.05260.00020.05250.00760.0508-0.1322-0.0195-0.05380.0017-0.09660.05030.0243-0.0238-0.0115-0.030665.09733.90359.38
161.0457-0.10310.06820.9377-0.412.7690.0179-0.1657-0.07130.02290.0039-0.29550.12890.1128-0.0218-0.0427-0.0014-0.02250.0292-0.0158-0.020968.75816.75674.91
176.17812.24572.15942.98761.41293.799-0.0166-0.23980.00980.03390.04140.20780.0568-0.4036-0.0247-0.06920.02960.00160.04390.0297-0.087657.35413.01776.617
183.787-1.22136.02586.97342.102515.60540.1003-0.0489-0.49890.69390.0049-0.04260.92540.2157-0.10530.0473-0.0371-0.01230.0030.0622-0.000161.3191.68876.701
190.7251-0.2582-0.0732.55420.41551.74450.0267-0.114-0.05590.06680.0345-0.06680.0198-0.2251-0.0612-0.08860.00770.00970.01960.001-0.049761.28718.92574.215
201.194-0.2591-0.54451.9073-1.50551.6724-0.0111-0.0355-0.1099-0.10550.0376-0.0170.1132-0.0704-0.0265-0.06610.0093-0.0022-0.0077-0.01-0.05263.14919.05567.728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA98 - 1191 - 22
2X-RAY DIFFRACTION2AA120 - 15623 - 59
3X-RAY DIFFRACTION3AA157 - 20460 - 107
4X-RAY DIFFRACTION4AA205 - 227108 - 130
5X-RAY DIFFRACTION5AA228 - 259131 - 162
6X-RAY DIFFRACTION6BB100 - 1243 - 27
7X-RAY DIFFRACTION7BB125 - 16828 - 71
8X-RAY DIFFRACTION8BB169 - 23072 - 133
9X-RAY DIFFRACTION9BB231 - 244134 - 147
10X-RAY DIFFRACTION10BB245 - 259148 - 162
11X-RAY DIFFRACTION11CC100 - 1223 - 25
12X-RAY DIFFRACTION12CC123 - 13926 - 42
13X-RAY DIFFRACTION13CC140 - 17643 - 79
14X-RAY DIFFRACTION14CC177 - 22880 - 131
15X-RAY DIFFRACTION15CC229 - 259132 - 162
16X-RAY DIFFRACTION16DD100 - 1243 - 27
17X-RAY DIFFRACTION17DD125 - 16428 - 67
18X-RAY DIFFRACTION18DD165 - 18268 - 85
19X-RAY DIFFRACTION19DD183 - 23086 - 133
20X-RAY DIFFRACTION20DD231 - 259134 - 162

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