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- PDB-5fgl: Co-crystal Structure of NicR2_Hsp -

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Basic information

Entry
Database: PDB / ID: 5fgl
TitleCo-crystal Structure of NicR2_Hsp
ComponentsNicR
KeywordsAPOPTOSIS / co-crystal derepression / Nicotine regulator 2
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
PsrA, tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily ...PsrA, tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhang, K. / Tang, H. / Wu, G. / Wang, W. / Hu, H. / Xu, P.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese National Natural Science Foundation31230002 China
Chinese National Natural Science Foundation31270154 China
Chinese National Science Foundation for Excellent Young Scholars31422004 China
CitationJournal: To Be Published
Title: Co-crystal Structure of NicR2_Hsp
Authors: Zhang, K. / Tang, H. / Wu, G. / Wang, W. / Hu, H. / Xu, P.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: NicR
B: NicR
C: NicR
D: NicR
E: NicR
F: NicR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,47912
Polymers144,3086
Non-polymers1,1716
Water3,387188
1
A: NicR
B: NicR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4934
Polymers48,1032
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-30 kcal/mol
Surface area18740 Å2
MethodPISA
2
C: NicR
D: NicR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4934
Polymers48,1032
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-29 kcal/mol
Surface area19090 Å2
MethodPISA
3
E: NicR
F: NicR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4934
Polymers48,1032
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-33 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.522, 149.522, 156.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHRAA30 - 2331 - 204
21METMETTHRTHRBB30 - 2331 - 204
12METMETALAALAAA30 - 2321 - 203
22METMETALAALACC30 - 2321 - 203
13METMETALAALAAA30 - 2321 - 203
23METMETALAALADD30 - 2321 - 203
14METMETTHRTHRAA30 - 2331 - 204
24METMETTHRTHREE30 - 2331 - 204
15GLUGLUTHRTHRAA31 - 2332 - 204
25GLUGLUTHRTHRFF31 - 2332 - 204
16METMETASPASPBB30 - 2351 - 206
26METMETASPASPCC30 - 2351 - 206
17METMETASPASPBB30 - 2351 - 206
27METMETASPASPDD30 - 2351 - 206
18METMETASPASPBB30 - 2351 - 206
28METMETASPASPEE30 - 2351 - 206
19GLUGLUALAALABB31 - 2322 - 203
29GLUGLUALAALAFF31 - 2322 - 203
110METMETGLNGLNCC30 - 2341 - 205
210METMETGLNGLNDD30 - 2341 - 205
111METMETASPASPCC30 - 2351 - 206
211METMETASPASPEE30 - 2351 - 206
112GLUGLUALAALACC31 - 2322 - 203
212GLUGLUALAALAFF31 - 2322 - 203
113METMETASPASPDD30 - 2351 - 206
213METMETASPASPEE30 - 2351 - 206
114GLUGLUALAALADD31 - 2322 - 203
214GLUGLUALAALAFF31 - 2322 - 203
115GLUGLUALAALAEE31 - 2322 - 203
215GLUGLUALAALAFF31 - 2322 - 203

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
NicR


Mass: 24051.293 Da / Num. of mol.: 6 / Fragment: UNP residues 31-237 / Mutation: G95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain S16) (bacteria)
Strain: S16 / Gene: nicR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4KIF6
#2: Chemical
ChemComp-6HY / 4-oxidanylidene-4-(6-oxidanylidene-1~{H}-pyridin-3-yl)butanoic acid


Mass: 195.172 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C9H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 1M Sodium malonate pH5.0, 0.1M Sodium acetate trihydrate pH4.5, 2%(w/v) polyethylene 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 64118 / % possible obs: 99.8 % / Redundancy: 8.2 % / Net I/σ(I): 17.6
Reflection shellRedundancy: 8.2 % / Mean I/σ(I) obs: 4.62 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 14.614 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22943 3426 5.1 %RANDOM
Rwork0.1999 ---
obs0.20137 61445 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.565 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9890 0 84 188 10162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910193
X-RAY DIFFRACTIONr_bond_other_d0.0050.029608
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.95813741
X-RAY DIFFRACTIONr_angle_other_deg1.16322035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.81251217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01124.004527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.697151818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6461575
X-RAY DIFFRACTIONr_chiral_restr0.0780.21479
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211554
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022447
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_it2.1213.5144880
X-RAY DIFFRACTIONr_mcbond_other2.123.5144881
X-RAY DIFFRACTIONr_mcangle_it3.3765.2546084
X-RAY DIFFRACTIONr_mcangle_other3.3765.2556085
X-RAY DIFFRACTIONr_scbond_it2.7673.875313
X-RAY DIFFRACTIONr_scbond_other2.7673.875314
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5115.6747654
X-RAY DIFFRACTIONr_long_range_B_refined6.43728.3712229
X-RAY DIFFRACTIONr_long_range_B_other6.41728.30812189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A121610.07
12B121610.07
21A122820.05
22C122820.05
31A122290.07
32D122290.07
41A122380.07
42E122380.07
51A123150.03
52F123150.03
61B121080.08
62C121080.08
71B122190.08
72D122190.08
81B122910.08
82E122910.08
91B120340.06
92F120340.06
101C122740.07
102D122740.07
111C122260.07
112E122260.07
121C122140.04
122F122140.04
131D123840.06
132E123840.06
141D121060.06
142F121060.06
151E120950.07
152F120950.07
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 256 -
Rwork0.251 4729 -
obs--98.79 %
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)
11.31250.0539-0.74223.6033-1.16032.4778-0.00780.4293-0.0209-0.165-0.0378-0.24320.10080.06530.04560.05330.0191-0.01680.1937-0.01690.033922.3468-9.5003-14.8339
22.12280.56630.37022.13981.28982.2912-0.0332-0.00460.09860.1963-0.11740.20510.1314-0.25910.15070.0762-0.0217-0.00510.04090.00390.052512.6814-10.37375.689
32.3166-0.70720.86621.1529-0.22244.02440.14830.1036-0.09550.0009-0.01-0.40190.10710.2035-0.13840.0229-0.0118-0.01920.058-0.03810.2127-3.3218-59.96312.2666
43.17840.6583-1.81112.32360.03372.39460.33090.26070.39830.037-0.12160.1066-0.474-0.3562-0.20930.10080.06630.02940.06420.03160.0653-23.1542-49.787511.4582
52.5913-1.30780.7261.8953-0.33041.78830.190.28190.1561-0.3141-0.1593-0.04820.00160.0051-0.03070.1210.0179-0.020.0508-0.00960.0954-11.573-28.00634.2845
62.62371.0868-0.55583.4903-0.09760.87220.073-0.16090.11240.0961-0.10750.2729-0.0281-0.35950.03450.07450.028-0.07970.2273-0.0720.1391-32.2244-27.900243.5924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 233
2X-RAY DIFFRACTION2B30 - 235
3X-RAY DIFFRACTION3C30 - 237
4X-RAY DIFFRACTION4D30 - 235
5X-RAY DIFFRACTION5E30 - 235
6X-RAY DIFFRACTION6F31 - 233

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