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- PDB-5gpe: Crystal structure of the transcription regulator PbrR691 from Ral... -

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Basic information

Entry
Database: PDB / ID: 5gpe
TitleCrystal structure of the transcription regulator PbrR691 from Ralstonia metallidurans CH34 in complex with Lead(II)
ComponentsTranscriptional regulator, MerR-family
KeywordsTRANSCRIPTION / PbrR691 / MerR family / Transcription activator
Function / homology
Function and homology information


DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Transcription regulator MerR, DNA binding / Cd(II)/Pb(II)-responsive transcriptional regulator / MerR, DNA binding / MerR family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
LEAD (II) ION / Transcriptional regulator, MerR-family
Similarity search - Component
Biological speciesCupriavidus metallidurans CH34 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHuang, S.Q. / Chen, W.Z. / Wang, D. / Hu, Q.Y. / Liu, X.C. / Gan, J.H. / Chen, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Inorg Chem / Year: 2016
Title: Structural Basis for the Selective Pb(II) Recognition of Metalloregulatory Protein PbrR691
Authors: Huang, S.Q. / Liu, X.C. / Wang, D. / Chen, W.Z. / Hu, Q.Y. / Wei, T.B. / Zhou, W.Q. / Gan, J.H. / Chen, H.
History
DepositionAug 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 15, 2021Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, MerR-family
B: Transcriptional regulator, MerR-family
C: Transcriptional regulator, MerR-family
D: Transcriptional regulator, MerR-family
E: Transcriptional regulator, MerR-family
F: Transcriptional regulator, MerR-family
G: Transcriptional regulator, MerR-family
H: Transcriptional regulator, MerR-family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,32516
Polymers119,6678
Non-polymers1,6588
Water8,377465
1
A: Transcriptional regulator, MerR-family
B: Transcriptional regulator, MerR-family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3314
Polymers29,9172
Non-polymers4142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-38 kcal/mol
Surface area14500 Å2
MethodPISA
2
C: Transcriptional regulator, MerR-family
D: Transcriptional regulator, MerR-family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3314
Polymers29,9172
Non-polymers4142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-37 kcal/mol
Surface area14990 Å2
MethodPISA
3
E: Transcriptional regulator, MerR-family
F: Transcriptional regulator, MerR-family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3314
Polymers29,9172
Non-polymers4142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-38 kcal/mol
Surface area14550 Å2
MethodPISA
4
G: Transcriptional regulator, MerR-family
H: Transcriptional regulator, MerR-family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3314
Polymers29,9172
Non-polymers4142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-38 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.938, 67.903, 89.723
Angle α, β, γ (deg.)109.33, 89.82, 90.32
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 129 / Label seq-ID: 1 - 129

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Transcriptional regulator, MerR-family


Mass: 14958.383 Da / Num. of mol.: 8 / Fragment: UNP residues 1-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans CH34 (bacteria)
Strain: CH34 / Gene: pbrR2, Rmet_2302 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q1LKZ5
#2: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Pb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Tacsimate, HEPES, PEG3350

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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: Dec 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 88839 / % possible obs: 95.9 % / Redundancy: 3.2 % / Rsym value: 0.11 / Net I/σ(I): 23.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.3 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D07

5d07
PDB Unreleased entry


Resolution: 2.01→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.923 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.142 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21356 4470 5 %RANDOM
Rwork0.17661 ---
obs0.17847 84363 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.445 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å2-0.47 Å2-0.31 Å2
2---2.29 Å20.48 Å2
3---2.61 Å2
Refinement stepCycle: 1 / Resolution: 2.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8159 0 8 465 8632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198228
X-RAY DIFFRACTIONr_bond_other_d0.0070.028318
X-RAY DIFFRACTIONr_angle_refined_deg1.3612.00210995
X-RAY DIFFRACTIONr_angle_other_deg1.581319005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4215995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76221.986423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.213151680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.87915142
X-RAY DIFFRACTIONr_chiral_restr0.0630.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029137
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021905
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_it2.0931.9034022
X-RAY DIFFRACTIONr_mcbond_other2.0941.9024021
X-RAY DIFFRACTIONr_mcangle_it2.7162.8315000
X-RAY DIFFRACTIONr_mcangle_other2.7152.8325001
X-RAY DIFFRACTIONr_scbond_it2.8892.4444206
X-RAY DIFFRACTIONr_scbond_other2.8812.4444206
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4943.495994
X-RAY DIFFRACTIONr_long_range_B_refined4.01515.299468
X-RAY DIFFRACTIONr_long_range_B_other3.84615.0069259
X-RAY DIFFRACTIONr_rigid_bond_restr4.482316546
X-RAY DIFFRACTIONr_sphericity_free27.8995142
X-RAY DIFFRACTIONr_sphericity_bonded9.731516813
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A139280.11
12B139280.11
21A141200.1
22C141200.1
31A143080.07
32D143080.07
41A144300.06
42E144300.06
51A138840.11
52F138840.11
61A144140.07
62G144140.07
71A139400.11
72H139400.11
81B144620.1
82C144620.1
91B144280.1
92D144280.1
101B137660.11
102E137660.11
111B146920.09
112F146920.09
121B142180.11
122G142180.11
131B147240.08
132H147240.08
141C145140.11
142D145140.11
151C140540.1
152E140540.1
161C147980.08
162F147980.08
171C147640.1
172G147640.1
181C148800.09
182H148800.09
191D143200.07
192E143200.07
201D146220.09
202F146220.09
211D150640.06
212G150640.06
221D148320.09
222H148320.09
231E139040.1
232F139040.1
241E144220.07
242G144220.07
251E139500.1
252H139500.1
261F144820.1
262G144820.1
271F150420.06
272H150420.06
281G145140.11
282H145140.11
LS refinement shellResolution: 2.008→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 282 -
Rwork0.216 5239 -
obs--79.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1033-0.10870.05310.1973-0.150.2219-0.0121-0.02610.00040.00490.0008-0.00050.01810.00040.01130.08740.00510.00640.10530.00030.001751.949412.856364.3366
20.02020.0081-0.04040.0681-0.03710.0891-0.0059-0.0019-0.001-0.00590.00750.00870.003-0.008-0.00160.08630.0011-0.00060.10780.00330.008646.85918.938545.6329
30.06030.0467-0.06960.2620.05890.146-0.0063-0.0053-0.01360.0156-0.0009-0.0265-0.00460.02560.00720.0777-0.00010.00370.1086-0.00240.008925.0833-15.208147.2246
40.11660.07560.0330.14010.12690.2419-0.01710.0253-0.0051-0.0037-0.00010.00770.02070.00740.01720.0872-0.00060.00710.10860.00140.002220.0609-21.814427.3577
50.08020.0684-0.03240.1158-0.11130.1807-0.01220.0206-0.002-0.0055-0.001-0.0027-0.0095-0.00360.01330.0899-0.00460.00210.10940.00080.003320.7937-12.720428.2821
60.0226-0.01630.04250.0723-0.05940.0948-0.0080.00070.00180.0060.00670.0079-0.0081-0.00850.00130.0843-0.00110.010.10540.00330.008815.3428-18.552647.0057
70.1131-0.08610.00110.11990.07690.1467-0.0232-0.02980.00720.00450.00030.0076-0.0203-0.00170.02290.08530.00340.00250.1103-0.00140.004951.341222.094265.0788
80.01390.00150.02720.10390.03660.0688-0.0077-0.00170.0032-0.00880.0044-0.01520.00240.00260.00330.08240.00190.00920.1073-0.00280.00856.380915.483645.2133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 129
2X-RAY DIFFRACTION2B1 - 129
3X-RAY DIFFRACTION3C1 - 129
4X-RAY DIFFRACTION4D1 - 129
5X-RAY DIFFRACTION5E1 - 129
6X-RAY DIFFRACTION6F1 - 129
7X-RAY DIFFRACTION7G1 - 129
8X-RAY DIFFRACTION8H1 - 129

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