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- PDB-4gpk: Crystal structure of NprR in complex with its cognate peptide NprX -

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Basic information

Entry
Database: PDB / ID: 4gpk
TitleCrystal structure of NprR in complex with its cognate peptide NprX
Components
  • NprR
  • NprX peptide
KeywordsTranscription / Peptide binding protein / TPR motif / Transcription factor / Quorum sensor / Transcription-Signaling peptide complex
Function / homology
Function and homology information


Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1000 / : / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus thuringiensis serovar thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsZouhir, S. / Guimaraes, B. / Perchat, S. / Nicaise, M. / Lereclus, D. / Nessler, S.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Peptide-binding dependent conformational changes regulate the transcriptional activity of the quorum-sensor NprR.
Authors: Zouhir, S. / Perchat, S. / Nicaise, M. / Perez, J. / Guimaraes, B. / Lereclus, D. / Nessler, S.
History
DepositionAug 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NprR
B: NprR
C: NprR
D: NprR
E: NprR
F: NprR
G: NprR
H: NprR
I: NprR
J: NprR
K: NprR
L: NprR
M: NprX peptide
N: NprX peptide
O: NprX peptide
P: NprX peptide
Q: NprX peptide
R: NprX peptide
S: NprX peptide
T: NprX peptide
U: NprX peptide
V: NprX peptide
W: NprX peptide
X: NprX peptide


Theoretical massNumber of molelcules
Total (without water)544,00924
Polymers544,00924
Non-polymers00
Water0
1
A: NprR
B: NprR
C: NprR
D: NprR
M: NprX peptide
N: NprX peptide
O: NprX peptide
P: NprX peptide


Theoretical massNumber of molelcules
Total (without water)181,3368
Polymers181,3368
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-61 kcal/mol
Surface area64800 Å2
2
E: NprR
F: NprR
G: NprR
H: NprR
Q: NprX peptide
R: NprX peptide
S: NprX peptide
T: NprX peptide


Theoretical massNumber of molelcules
Total (without water)181,3368
Polymers181,3368
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13670 Å2
ΔGint-62 kcal/mol
Surface area66530 Å2
3
I: NprR
J: NprR
K: NprR
L: NprR
U: NprX peptide
V: NprX peptide
W: NprX peptide
X: NprX peptide


Theoretical massNumber of molelcules
Total (without water)181,3368
Polymers181,3368
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14150 Å2
ΔGint-68 kcal/mol
Surface area67050 Å2
Unit cell
Length a, b, c (Å)122.240, 133.350, 137.500
Angle α, β, γ (deg.)108.25, 104.83, 103.83
Int Tables number1
Space group name H-MP1
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS A TETRAMER OF NPRR, WITH A PEPTIDE BOUND IN EACH SUBUNIT.

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Components

#1: Protein
NprR


Mass: 44531.219 Da / Num. of mol.: 12
Fragment: THIS IS A TRUNCATED FORM OF THE FULL-LENGTH PROTEIN, MISSING THE 60 RESIDUES OF THE N-TERMINAL HTH DOMAIN, AND WITH AN ADDITIONAL C-TERMINAL HIS-TAG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar thuringiensis (bacteria)
Gene: nprR / Production host: Escherichia coli (E. coli) / References: UniProt: G5DDY8
#2: Protein/peptide
NprX peptide


Mass: 802.894 Da / Num. of mol.: 12 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.975M Natrium Citrate, 0.1M HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.97918
SYNCHROTRONSOLEIL PROXIMA 120.98011
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDFeb 3, 2010
DECTRIS PILATUS 6M2PIXELNov 27, 2011Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1channel cut Si111SINGLE WAVELENGTHMx-ray1
2channel cut Si111SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.980111
ReflectionNumber: 715889 / Rmerge(I) obs: 0.098 / D res high: 3.47 Å / Num. obs: 187712 / % possible obs: 96.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
3.473.682778888.410.706
3.683.932884097.810.442
3.934.242689097.810.243
4.244.642473297.910.127
4.645.182238097.810.105
5.185.971982697.910.112
5.977.281677597.510.07
7.2810.161301497.410.041
ReflectionResolution: 3.09→50 Å / Num. all: 132686 / Num. obs: 132663 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 110.33 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.87
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.09-3.280.6431.951,294.5
3.28-3.510.2744.571,297.5
3.51-3.790.1358.851,297.6
3.79-4.140.07515.341,297.8
4.14-4.630.04624.291,297.8
4.63-5.340.04128.271,297.6
5.34-6.520.0430.021,297.6
6.52-9.140.03137.561,297.1
9.14-500.02940.61,295.4

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
168.81554.22699.678S201
265.57460.29120.077S200.82
387.09426.15173.068S200.814
464.81422.494108.774S200.806
563.90765.689130.322S200.795
624.21955.673145.395S200.793
757.3330.684111.052S200.782
8117.3331.86176.295S200.775
989.94823.749123.728S200.77
1073.29951.68489.813S200.736
1138.27178.591169.753S200.721
1232.2372.483176.102S200.719
1359.69760.018102.722S200.716
1477.85927.372166.611S200.708
1528.68161.933174.412S200.708
1633.17151.039116.335S200.705
1794.524-1.66156.574S200.704
1814.46664.688157.07S200.702
1919.61477.412140.672S200.693
2039.09543.65287.986S200.684
21112.96410.031169.543S200.679
2242.35645.306113.039S200.667
2333.338115.963181.315S200.663
2459.81430.988137.411S200.657
2523.85787.091157.249S200.655
2638.95390.88183.01S200.651
271.84785.603174.362S200.637
28109.48826.455156.918S200.622
2929.58274.74599.531S200.621
30103.47529.588186.452S200.616
31-1.70184.896202.923S200.591
3297.899-14.327187.714S200.582
3373.1323.078150.612S200.581
34103.4110.815163.303S200.575
3521.47489.249202.543S200.573
3629.62986.822187.54S200.569
3750.49571.3893.072S200.569
3822.14183.963205.518S200.566
3950.39473.737158.384S200.554
4027.14797.906158.461S200.553
4171.30951.03117.478S200.548
4246.94543.648103.131S200.547
4351.4776.94894.753S200.546
4434.864104.711153.58S200.542
45133.29936.311167.821S200.542
4624.78878.186143.428S200.54
4710.98289.778170.054S200.535
4852.69594.76158.538S200.534
4985.80654.4383.995S200.534
50128.75139.132168.291S200.525
5191.50117.543178.162S200.514
5220.86582.47688.232S200.509
5371.99688.391115.752S200.508
5484.60116.26148.281S200.504
5517.18998.028174.654S200.5
56116.329.093166.108S200.499
5783.3933.498184.355S200.488
5850.65451.114140.475S200.488
5984.14231.65109.604S200.487
6095.069-2.61150.244S200.487
61106.42353.657178.964S200.467
6256.9336.8120.858S200.463
6340.10271.621112.627S200.461
64107.79962.071158.82S200.458
65105.0231.592192.433S200.454
66102.93935.584178.403S200.449
6745.82299.231187.504S200.447
6854.86229.874140.117S200.446
69-12.64482.524166.459S200.442
7032.439118.112147.063S200.441
7182.9332.691189.46S200.441
7265.10780.145132.398S200.441
7339.82957.456199.516S200.437
7485.5445.201126.324S200.435
7596.62264.89699.164S200.434
7628.88350.606183.981S200.433
7790.28545.934124.137S200.428
7859.89736.35783.162S200.426
7961.5759.842102.805S200.418
8021.30947.962125.29S200.417
81100.05109.842132.047S200.415
8283.19774.777107.637S200.414
8367.69437.944167.905S200.41
8424.53327.735129.137S200.41
851.30681.39488.575S200.407
8653.45846.55770.173S200.395
8737.59937.42585.585S200.395
8855.57374.057160.06S200.394
8911.915110.015184.583S200.392
9034.43523.225117.564S200.389
91116.56113.249131.344S200.386
92128.06227.357187.441S200.385
93109.4531.765133.903S200.384
9415.35599.973188.985S200.379
95133.98144.492189.719S200.366
96109.06229.534196.114S200.355
9749.83272.621171.381S200.351
98111.68759.546155.242S200.35
99100.62656.693179.253S200.348
100-5.49589.12173.623S200.343
1013.786106.082153.279S200.33
10288.546.343198.233S200.324
103-1.11678.05981.027S200.316
10411.483115.585182.534S200.311
10541.7299.39101.14S200.309
10662.55147.181152.144S200.306
107138.461.8156.681S200.302
108-8.98392.257148.526S200.297
10931.4935.65582.097S200.294
11014.481122.182150.104S200.293
11127.941101.535118.993S200.289
11258.449106.499159.808S200.289
11347.09969.756194.322S200.289
11496.02119.673190.58S200.282
115137.33249.193202.196S200.282
11648.24794.266137.062S200.282
11795.14544.81474.762S200.282
118-20.1876.003179.689S200.279
119132.403-3.685174.839S200.277
12053.26224.461130.497S200.276
12148.776-0.949114.504S200.271
12230.701-21.969107.708S200.27
12393.73911.061187.963S200.267
12416.68860.228169.763S200.266
12549.29640.21998.07S200.265
126106.3718.45193.434S200.261
12754.09578.021204.01S200.261
128104.23822.528156.864S200.26
12911.332101.489199.259S200.258
13094.65248.653158.354S200.257
1317.75275.724192.369S200.256
132108.84411.974111.26S200.249
13325.19393.121163.447S200.247
13456.37876.953148.753S200.247
135107.93634.5148.561S200.245
13697.94862.38591.942S200.244
13786.54971.616120.917S200.243
13882.172-7.465172.728S200.239
13992.27264.617177.774S200.238
14033.99375.964204.19S200.237
14146.03576.289168.303S200.23
14292.536-29.48189.759S200.227
143104.752125.368136.933S200.226
144118.23949.855155.28S200.219
14551.18254.55564.224S200.218
146149.52738.543212.724S200.218
147114.36825.107187.804S200.217
14825.15173.364128.639S200.206
14950.7324.874137.466S200.206
15095.57117.046116.106S200.205
15127.501102.789169.889S200.205
152-4.79487.403191.246S200.204
15351.92472.238194.32S200.203
154122.494-4.997154.779S200.197
15519.24899.039209.285S200.193
15627.4787.683172.701S200.192
15729.79105.29150.006S200.189
158145.062-5.967153.063S200.188
159113.95740.72162.012S200.187
16022.58974.689167.002S200.187
16138.663-14.67283.22S200.186
162132.0923.649165.824S200.185
16348.60963.056125.929S200.184
16413.01666.019107.555S200.184
16569.61543.233126.125S200.182
16644.49224.62180.009S200.181
167-29.93999.624168.129S200.18
16816.68365.053148.518S200.178
16972.527-1.242183.129S200.177
17019.58155.985151.14S200.175
171-11.625101.107172.352S200.174
17246.18113.408103.94S200.173
173136.80538.869210.723S200.172
174133.83225.29181.243S200.158
17577.4212.122186.007S200.157
17612.54640.239149.914S200.154
17785.683.766174.682S200.152
178-4.95784.96886.313S200.15
17917.21866.817118.809S200.149
18043.57347.05984.802S200.147
181153.43-7.412146.955S200.145
18260.13542.33962.395S200.142
18384.06467.276163.657S200.14
18446.2125.729184.717S200.14
18538.377-25.84196.712S200.137
18692.925-14.406192.96S200.131
187106.00619.29999.619S200.13
188107.14958.509109.691S200.13
1892.73773.80792.803S200.129
19024.47431.005122.18S200.122
191128.29139.064176.531S200.104
19240.85114.951197.656S200.091
19358.8251.241215.819S200.091
194-8.37182.209129.272S200.081
195-15.211100.663179.601S200.064
19633.75646.6471.836S200.02
Phasing dmFOM : 0.78 / FOM acentric: 0.78 / FOM centric: 0 / Reflection: 94307 / Reflection acentric: 94307 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
9.9-44.4480.940.9440424042
6.2-9.90.910.911276812768
5-6.20.820.821600216002
4.3-50.810.811623416234
3.7-4.30.720.722874828748
3.5-3.70.660.661651316513

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
SHELXphasing
RESOLVE2.13phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
SHELXDphasing
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→29.736 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9327 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.51 / σ(F): 1.99 / Phase error: 34.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2994 24324 20 %
Rwork0.2695 --
obs0.2755 121622 98.46 %
all-132655 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 159.96 Å2
Baniso -1Baniso -2Baniso -3
1--15.7013 Å2-0.4954 Å2-4.416 Å2
2--2.7796 Å25.4622 Å2
3---12.9218 Å2
Refine analyzeLuzzati coordinate error obs: 1.42 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35360 0 0 0 35360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236040
X-RAY DIFFRACTIONf_angle_d0.63248431
X-RAY DIFFRACTIONf_dihedral_angle_d12.48313753
X-RAY DIFFRACTIONf_chiral_restr0.055230
X-RAY DIFFRACTIONf_plane_restr0.0026029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23310.39767470.34932990X-RAY DIFFRACTION91
3.2331-3.27110.40048120.34933248X-RAY DIFFRACTION99
3.2711-3.3110.37958110.3223243X-RAY DIFFRACTION98
3.311-3.35280.36758170.32093269X-RAY DIFFRACTION99
3.3528-3.39690.35048080.3163230X-RAY DIFFRACTION99
3.3969-3.44330.37378150.31513262X-RAY DIFFRACTION99
3.4433-3.49250.35858150.3253259X-RAY DIFFRACTION99
3.4925-3.54450.36428090.31563235X-RAY DIFFRACTION99
3.5445-3.59980.35418280.30793311X-RAY DIFFRACTION99
3.5998-3.65870.32787960.31243187X-RAY DIFFRACTION99
3.6587-3.72170.34028170.29443265X-RAY DIFFRACTION99
3.7217-3.78920.35758170.30783267X-RAY DIFFRACTION99
3.7892-3.8620.3538130.30653253X-RAY DIFFRACTION99
3.862-3.94060.34738220.30543285X-RAY DIFFRACTION99
3.9406-4.02610.33258060.29773227X-RAY DIFFRACTION99
4.0261-4.11950.34668070.29773230X-RAY DIFFRACTION99
4.1195-4.22230.29798190.28383277X-RAY DIFFRACTION99
4.2223-4.33610.31288080.28953233X-RAY DIFFRACTION99
4.3361-4.46330.31168230.28213288X-RAY DIFFRACTION99
4.4633-4.60680.29778160.26983264X-RAY DIFFRACTION99
4.6068-4.77080.29438210.26933286X-RAY DIFFRACTION99
4.7708-4.9610.32128160.27123263X-RAY DIFFRACTION99
4.961-5.18570.31838070.28963231X-RAY DIFFRACTION99
5.1857-5.45750.34098170.29453265X-RAY DIFFRACTION99
5.4575-5.79710.33798110.32183243X-RAY DIFFRACTION99
5.7971-6.24090.35758130.31693252X-RAY DIFFRACTION99
6.2409-6.86190.31478130.28053256X-RAY DIFFRACTION98
6.8619-7.83890.24878090.22923236X-RAY DIFFRACTION99
7.8389-9.81680.20478100.19363237X-RAY DIFFRACTION98
9.8168-29.73730.23758010.21793206X-RAY DIFFRACTION97

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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