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- PDB-5crl: Crystal Structure of the Transcription Activator Tn501 MerR in Co... -

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Basic information

Entry
Database: PDB / ID: 5crl
TitleCrystal Structure of the Transcription Activator Tn501 MerR in Complex with Mercury (II)
ComponentsMercuric resistance operon regulatory protein
KeywordsMETAL BINDING PROTEIN / transcription activator / MerR / mercury / P. aeruginosa Tn501
Function / homology
Function and homology information


mercury ion binding / response to mercury ion / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Hg(II)-responsive transcriptional regulator / Transcription regulator MerR, DNA binding / MerR, DNA binding / MerR family regulatory protein / MerR-type HTH domain signature. / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
: / Mercuric resistance operon regulatory protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsWang, D. / Gan, J.H. / Chen, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Sci Rep / Year: 2016
Title: Structural Analysis of the Hg(II)-Regulatory Protein Tn501 MerR from Pseudomonas aeruginosa.
Authors: Wang, D. / Huang, S. / Liu, P. / Liu, X. / He, Y. / Chen, W. / Hu, Q. / Wei, T. / Gan, J. / Ma, J. / Chen, H.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Apr 12, 2023Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ncs_dom_lim.pdbx_component_id / _struct_ncs_dom_lim.pdbx_refine_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mercuric resistance operon regulatory protein
B: Mercuric resistance operon regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2854
Polymers29,8842
Non-polymers4012
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-104 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.011, 75.011, 97.761
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 7 - 133 / Label seq-ID: 7 - 133

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

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Components

#1: Protein Mercuric resistance operon regulatory protein


Mass: 14942.152 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: merR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P0A183
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M KCl, 0.01M MgCl2, 0.1M Tris (pH 8.5), 30% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 7897 / % possible obs: 96.3 % / Redundancy: 5.5 % / Rsym value: 0.06 / Net I/σ(I): 43
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.77 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / SU B: 33.979 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R: 1.688 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26629 366 4.6 %RANDOM
Rwork0.22991 ---
obs0.2316 7531 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-1.12 Å20 Å2
2---1.12 Å20 Å2
3---3.62 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 2 1 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191831
X-RAY DIFFRACTIONr_bond_other_d0.0030.021840
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.9792445
X-RAY DIFFRACTIONr_angle_other_deg0.8813.0034196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7655228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10822.61984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86315345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.571522
X-RAY DIFFRACTIONr_chiral_restr0.050.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022034
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02416
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6152 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.801→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 32 -
Rwork0.315 519 -
obs--93.71 %
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)
10.83540.6695-0.17781.1817-1.40983.7704-0.2397-0.0695-0.07570.05910.1576-0.0369-0.4003-0.0070.08220.5073-0.0202-0.11540.3761-0.04060.27760.041322.4484-17.097
21.42321.79350.20362.91570.82050.83760.0420.0130.17120.3255-0.03680.3292-0.0332-0.204-0.00520.38350.10160.07120.4608-0.07220.3022-11.89624.43720.2144
34.225-0.0125-2.32263.08050.60561.4075-0.07670.01920.03590.2218-0.06240.50450.1218-0.01020.13910.2286-0.00210.08340.6841-0.22750.3414-37.812-4.2625-4.1596
40.45790.46490.04770.54020.06410.5527-0.00210.1071-0.06880.1001-0.0232-0.0459-0.0491-0.14640.02530.37320.03560.02190.52-0.06620.2718-9.83330.5095-4.3231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 63
2X-RAY DIFFRACTION2A64 - 133
3X-RAY DIFFRACTION3B7 - 63
4X-RAY DIFFRACTION4B64 - 134

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