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- PDB-5ed4: Structure of a PhoP-DNA complex -

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Basic information

Entry
Database: PDB / ID: 5ed4
TitleStructure of a PhoP-DNA complex
Components
  • (DNA (26-MER)) x 2
  • Response regulator
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / winged helix-turn-helix / direct repeat / tandem dimer / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


protein secretion by the type VII secretion system / glycolipid biosynthetic process / phosphorelay response regulator activity / phosphorelay signal transduction system / positive regulation of lipid biosynthetic process / protein-DNA complex / response to oxidative stress / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription ...protein secretion by the type VII secretion system / glycolipid biosynthetic process / phosphorelay response regulator activity / phosphorelay signal transduction system / positive regulation of lipid biosynthetic process / protein-DNA complex / response to oxidative stress / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription / DNA binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / DNA / DNA (> 10) / DNA-binding response regulator / Possible two component system response transcriptional positive regulator PhoP
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079185 United States
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis of DNA sequence recognition by the response regulator PhoP in Mycobacterium tuberculosis.
Authors: He, X. / Wang, L. / Wang, S.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Response regulator
B: Response regulator
C: DNA (26-MER)
D: DNA (26-MER)
E: Response regulator
F: Response regulator
G: DNA (26-MER)
H: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,96019
Polymers143,3348
Non-polymers62611
Water4,197233
1
A: Response regulator
B: Response regulator
C: DNA (26-MER)
D: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,97310
Polymers71,6674
Non-polymers3066
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-65 kcal/mol
Surface area27330 Å2
MethodPISA
2
E: Response regulator
F: Response regulator
G: DNA (26-MER)
H: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9869
Polymers71,6674
Non-polymers3195
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-59 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.240, 98.176, 167.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABEF

#1: Protein
Response regulator / / PhoP family transcriptional regulator


Mass: 27846.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: phoP, ABI38_13965, AC434_12840, BN1303_02986, ERS024750_01197, ERS024751_02016, ERS024758_01633, ERS124824_03492, ERS124825_03677, ERS124827_03481, ERS124828_03492, ERS124829_03387, ERS124830_ ...Gene: phoP, ABI38_13965, AC434_12840, BN1303_02986, ERS024750_01197, ERS024751_02016, ERS024758_01633, ERS124824_03492, ERS124825_03677, ERS124827_03481, ERS124828_03492, ERS124829_03387, ERS124830_03452, ERS124831_03570, ERS124832_03594, IQ38_16185, IQ42_15805, IQ45_15620, IQ47_15575, IQ48_15690, IU13_15815, IU15_16135, IU16_15745, IU17_15635, IU21_16005, T209_15560
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A045J469, UniProt: P71814*PLUS, alkaline phosphatase

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DNA chain , 2 types, 4 molecules CGDH

#2: DNA chain DNA (26-MER)


Mass: 7931.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 8042.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 244 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 50 mM sodium cacodylate, pH 6.5, 10 mM calcium chloride, 12% PEG4000, 2 mM spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 55326 / % possible obs: 90 % / Redundancy: 11.6 % / Biso Wilson estimate: 67.95 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.033 / Rrim(I) all: 0.117 / Χ2: 1.618 / Net I/av σ(I): 29.357 / Net I/σ(I): 9.7 / Num. measured all: 639291
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.446.10.7122.1316420.9320.2790.7681.00654.2
2.44-2.496.60.74918140.890.2820.8041.03760.2
2.49-2.537.60.65420080.9040.2320.6971.02665.7
2.53-2.598.40.57421470.9430.1930.6081.07171
2.59-2.649.10.56823640.940.1840.5991.08677.8
2.64-2.79.70.51625750.9530.1610.5421.12684.9
2.7-2.7710.10.48827180.9680.1510.5111.12989.4
2.77-2.8511.10.44629170.9760.1340.4671.1796.2
2.85-2.9311.80.34130260.9910.1010.3561.24199.2
2.93-3.0212.50.3130450.9910.0910.3241.279100
3.02-3.1313.50.24330550.9950.070.2531.353100
3.13-3.2613.20.17430420.9940.0530.1831.52799.8
3.26-3.412.70.15330720.9890.0470.161.64399.8
3.4-3.5813.30.13130590.9940.0390.1371.78899.9
3.58-3.81130.1230600.9960.0350.1262.051100
3.81-4.113.30.1131070.9960.0320.1152.238100
4.1-4.5112.80.09930900.9960.0290.1032.141100
4.51-5.16130.09231260.9960.0270.0962.15499.9
5.16-6.49130.08831530.9970.0250.0911.966100
6.49-3012.30.0833060.9960.0240.0841.95100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER-TNTBUSTER 2.10.2refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3R0J & 1GXP

3r0j

1gxp


Resolution: 2.4→29.6 Å / Cor.coef. Fo:Fc: 0.9223 / Cor.coef. Fo:Fc free: 0.9084 / SU R Cruickshank DPI: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.331 / SU Rfree Blow DPI: 0.228 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2793 5.05 %RANDOM
Rwork0.1827 52468 --
obs0.1849 55261 89.38 %-
Displacement parametersBiso max: 213.48 Å2 / Biso mean: 86.86 Å2 / Biso min: 45.35 Å2
Baniso -1Baniso -2Baniso -3
1--28.4723 Å20 Å20 Å2
2---0.7463 Å20 Å2
3---29.2186 Å2
Refine analyzeLuzzati coordinate error obs: 0.311 Å
Refinement stepCycle: final / Resolution: 2.4→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6937 2120 27 233 9317
Biso mean--106.54 75.84 -
Num. residues----981
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3018SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes163HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1143HARMONIC5
X-RAY DIFFRACTIONt_it9456HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1212SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9895SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9456HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg13247HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion21.53
LS refinement shellResolution: 2.4→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3026 103 4.76 %
Rwork0.2229 2061 -
all0.2263 2164 -
obs--47.71 %
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)
13.1159-0.9077-0.35385.22492.79845.2773-0.00620.1647-0.1901-0.0314-0.02170.21060.1852-0.07860.0279-0.0489-0.05580.0237-0.29470.0266-0.1733-48.671725.205112.5583
22.7166-0.31860.34712.86470.31044.85270.0811-0.0718-0.0717-0.0304-0.00910.4030.2011-0.2178-0.0721-0.0272-0.02280.0854-0.24670.0021-0.1883-40.45521.30532.816
33.1469-0.8513-1.77428.2620.26999.14210.14750.08290.28850.2865-0.34510.2859-1.3035-0.46080.19760.04950.0691-0.0049-0.3268-0.0027-0.2886-39.407625.0322-17.7279
44.6049-0.2779-0.48963.673-0.18485.2215-0.08410.5434-0.0463-0.51160.02480.62490.6478-0.91140.0593-0.0931-0.1287-0.0325-0.1487-0.0237-0.2665-36.20660.8491-30.7471
51.3489-0.0665-1.32940.79090.21268.59850.20010.08880.0379-0.12120.2665-0.18250.81140.7366-0.46660.1754-0.01170.0258-0.024-0.0004-0.2118-21.3273-1.4935-17.638
60.82290.27750.12750.5932-0.06424.76020.12180.1317-0.0145-0.18740.1778-0.09040.30590.8058-0.29960.24560.03780.03990.0788-0.0813-0.2318-19.7097-1.6901-20.4689
71.05160.40580.76473.64323.22466.1419-0.02350.0755-0.06990.0056-0.16030.22830.0894-0.29930.1837-0.0325-0.01310.0158-0.2407-0.0804-0.2007-79.8317-25.1322-43.2805
83.1593-1.1177-0.46922.7269-0.11943.64560.27210.283-0.1559-0.3185-0.10470.224-0.0052-0.1315-0.1675-0.06820.008-0.0684-0.2-0.0534-0.1735-81.7323-1.4182-29.7899
90.5212-0.30940.87255.5196-1.09319.96360.15990.0295-0.0145-0.1871-0.0502-0.07430.50240.6716-0.10970.01860.0276-0.0819-0.30590.0057-0.2366-77.2787-27.3573-12.6446
103.57180.59651.18883.3486-0.81317.78990.1199-0.23910.10590.78140.09120.5379-0.0168-0.802-0.21110.118-0.04440.0443-0.2277-0.0114-0.2787-85.1771-6.5264.149
111.3562-0.1-0.53771.5953-0.48939.31990.3818-0.29520.05550.46450.2072-0.3072-0.65230.8829-0.58910.0359-0.1133-0.1292-0.0264-0.0645-0.2176-68.66651.656-3.9679
121.3716-0.5924-0.53331.28820.73753.85620.1351-0.28730.0690.51760.183-0.242-0.0131.2812-0.31820.1235-0.1509-0.07120.0666-0.1358-0.2282-67.69871.5323-1.2235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|18 - 140 }A18 - 140
2X-RAY DIFFRACTION2{ A|149 - 247 }A149 - 247
3X-RAY DIFFRACTION3{ B|18 - 140 }B18 - 140
4X-RAY DIFFRACTION4{ B|149 - 247 }B149 - 247
5X-RAY DIFFRACTION5{ C|* }C1 - 26
6X-RAY DIFFRACTION6{ D|* }D1 - 26
7X-RAY DIFFRACTION7{ E|18 - 140 }E18 - 140
8X-RAY DIFFRACTION8{ E|147 - 247 }E147 - 247
9X-RAY DIFFRACTION9{ F|19 - 140 }F19 - 140
10X-RAY DIFFRACTION10{ F|149 - 247 }F149 - 247
11X-RAY DIFFRACTION11{ G|* }G1 - 26
12X-RAY DIFFRACTION12{ H|* }H1 - 26

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