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- PDB-7mrx: Cryogenic crystal structure of barnase A43C/S80C bound to barstar... -

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Basic information

Entry
Database: PDB / ID: 7mrx
TitleCryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/C82A
Components
  • Barstar
  • Ribonuclease
KeywordsRNA BINDING PROTEIN/Inhibitor / Disulfides / Toxin / antitoxin / RNA BINDING PROTEIN-Inhibitor complex
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region / cytoplasm
Similarity search - Function
Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase / Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Ribonuclease/ribotoxin
Similarity search - Domain/homology
Ribonuclease / Barstar
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.29 Å
AuthorsCaro, J.A. / Smith, J. / Wand, A.J.
CitationJournal: To Be Published
Title: Conformational entropy and protein affinity
Authors: Caro, J.A. / Wand, A.J.
History
DepositionMay 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease
B: Barstar
C: Ribonuclease
D: Barstar
E: Ribonuclease
F: Barstar


Theoretical massNumber of molelcules
Total (without water)74,3006
Polymers74,3006
Non-polymers00
Water6,503361
1
A: Ribonuclease
B: Barstar


Theoretical massNumber of molelcules
Total (without water)24,7672
Polymers24,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ribonuclease
D: Barstar


Theoretical massNumber of molelcules
Total (without water)24,7672
Polymers24,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ribonuclease
F: Barstar


Theoretical massNumber of molelcules
Total (without water)24,7672
Polymers24,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.317, 87.860, 162.492
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease / / Barnase / RNase Ba


Mass: 14478.056 Da / Num. of mol.: 3 / Mutation: A43C, S80C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Protein Barstar / / Ribonuclease inhibitor


Mass: 10288.608 Da / Num. of mol.: 3 / Mutation: C41A, C83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P11540
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.63 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50mM NaPO4, 25% PEG 8K, 0.1M AmSO4 4uL protein at 10-15 mg/mL in H2O + 4uL motherliquor per hanging drop, over 1 mL motherliquor in well. cryoprotectant used before freezing was: 25% MPD
PH range: 6-9

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Data collection

DiffractionMean temperature: 80 K
Ambient temp details: Collection under stream of liquid nitrogen
Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 1, 2016 / Details: Osmic VariMax mirror optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 33166 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.12 Å2 / Rmerge(I) obs: 0.066 / Χ2: 2.09 / Net I/σ(I): 15.5 / Num. measured all: 158662
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.29-2.333.30.24315981.128199.3
2.33-2.374.20.24216251.223199.8
2.37-2.424.80.22116471.284199.8
2.42-2.475.20.22416251.2141100
2.47-2.525.20.19716541.314199.9
2.52-2.585.10.18116121.388199.9
2.58-2.645.10.16216551.4741100
2.64-2.725.10.14716211.6011100
2.72-2.795.10.12816551.781199.9
2.79-2.8950.11516322.005199.8
2.89-2.995.10.10216432.184199.7
2.99-3.1150.08816392.432199.9
3.11-3.254.90.0816742.578199.7
3.25-3.424.80.06716472.684199.8
3.42-3.634.70.05916652.867199.6
3.63-3.924.60.05316782.899199.6
3.92-4.314.50.04816552.945199.7
4.31-4.934.40.04416982.879199.6
4.93-6.214.50.04517242.739199.7
6.21-5050.04218192.957198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å29.83 Å
Translation3 Å29.83 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.5.5phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2za4
Resolution: 2.29→29.83 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2293 1676 5.08 %
Rwork0.1828 31300 -
obs0.1852 32976 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.56 Å2 / Biso mean: 44.103 Å2 / Biso min: 21.81 Å2
Refinement stepCycle: final / Resolution: 2.29→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4741 0 0 361 5102
Biso mean---38.36 -
Num. residues----591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.360.29681530.22512421257495
2.36-2.430.31171460.220725712717100
2.43-2.520.30081520.230126012753100
2.52-2.620.27771330.22962566269999
2.62-2.740.29821480.2252574272299
2.74-2.880.29421510.22942563271499
2.88-3.060.30631280.20472594272299
3.06-3.30.24791430.20972608275199
3.3-3.630.20481330.1882638277199
3.63-4.160.20241210.15332660278199
4.16-5.230.15771370.139126662803100
5.23-29.830.17671310.155128382969100
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)
12.3007-0.12610.75773.5566-1.06132.8590.12-0.1185-0.37260.13510.0285-0.19630.4060.2142-0.13110.3424-0.0112-0.08680.37460.07870.2764-14.3136-48.917230.869
23.0792-0.70860.46192.426-0.81952.92290.0232-0.1493-0.61770.14180.00260.24610.4076-0.1846-0.2820.366-0.0821-0.0860.3560.09980.4259-22.1744-49.606526.3578
34.7517-0.5765-0.07822.024-0.5762.70560.24180.198-0.0129-0.2930.28040.8842-0.0572-0.4038-0.40.3018-0.0363-0.08290.32420.0960.4222-31.6817-43.09918.9047
43.57930.54730.12642.1008-0.69964.48220.2997-0.04450.36790.01560.26080.4677-0.3798-0.5572-0.28820.27440.0905-0.01030.39830.08830.3858-32.102-33.322221.0839
53.06251.00960.4621.8449-1.6624.00660.0918-0.7245-0.23610.53760.28790.4196-0.3303-0.2682-0.33140.31020.04320.05770.42180.12670.2848-30.9284-39.324628.7352
62.1135-0.42550.45241.5813-0.88462.21820.14930.2789-0.3503-0.3537-0.0010.06780.48580.209-0.12120.3350.0739-0.02230.316-0.01220.291-16.6951-42.955213.5675
72.8531-0.12310.30352.1683-1.13773.08080.27810.4044-0.3885-0.5132-0.2889-0.14410.58060.2628-0.05120.47930.1304-0.07740.3229-0.00750.2743-10.9095-47.784314.5513
82.5644-0.76540.67022.7659-0.90942.37730.0921-0.12810.25890.23960.053-0.17950.00670.0627-0.08570.2806-0.0093-0.06250.29410.02960.2292-18.6447-37.887124.8013
91.8367-0.24760.532.6403-1.02221.99070.2408-0.0704-0.1074-0.1482-0.1466-0.08360.29360.6969-0.01990.34980.1133-0.07590.36320.05080.3227-8.8836-48.535620.8904
102.5077-0.00760.54782.6356-1.45063.47120.16940.0990.07330.1122-0.1615-0.37090.22480.12510.11520.318-0.0299-0.11150.34070.02190.2987-8.1714-38.595120.7699
117.21470.9665-1.21510.2474-0.15550.31760.09010.03850.5131-0.35460.00980.2448-0.1627-0.2252-0.05840.3283-0.04180.02050.42180.07620.3107-21.1787-20.83892
122.49710.4412-0.07842.1897-0.4492.73720.10680.0010.0070.33270.0792-0.0948-0.14290.1052-0.16510.30030.0132-0.04270.30150.03450.2364-17.5518-28.277611.5651
133.1660.5610.10112.3831-0.51332.7913-0.06450.54120.0616-0.23560.2793-0.0649-0.2256-0.099-0.16420.3528-0.0158-0.01810.33480.05130.2679-20.4496-26.75470.7314
144.21.5254-0.26213.2735-0.73642.48430.00380.3241-0.53450.11850.2913-0.26120.91650.083-0.20770.3660.0472-0.06160.33230.00530.2701-20.6875-35.71161.5843
153.06451.056-0.49632.9659-0.79483.60080.1617-0.0947-0.3225-0.03810.04990.05580.2739-0.2216-0.27480.3514-0.0089-0.03670.44090.07750.3202-28.8264-32.89131.4114
163.2069-0.26530.67112.69920.12482.91690.1211-0.34770.29750.15680.0419-0.39070.16070.4294-0.08020.30110.0137-0.03010.3892-0.09620.291214.7343-4.763542.427
173.47211.1240.35593.6507-0.0462.0190.0660.1143-0.06360.06550.076-0.30180.44010.3173-0.20490.38080.0611-0.05060.3513-0.04430.310115.156-12.285937.5034
181.81340.42370.28556.5738-0.71952.56890.32210.4618-0.691-0.45520.05020.04810.8971-0.1183-0.34590.40690.063-0.12820.3834-0.04350.41968.3395-20.810429.2972
192.93340.01850.88093.19110.08673.04310.2799-0.077-0.6528-0.21190.0520.12950.9333-0.1327-0.26880.4382-0.0427-0.13250.2740.00360.37143.6582-18.371733.8237
202.64980.05820.55683.19950.05442.8934-0.11-0.0105-0.0225-0.30670.066-0.01450.08040.0986-0.04150.2704-0.0031-0.01820.2868-0.02310.21728.571-4.001329.1947
212.93170.04910.8762.67780.22522.6507-0.19130.33810.3308-0.05140.0579-0.1471-0.2549-0.01490.03110.3107-0.0101-0.03690.2789-0.04470.25210.29711.249532.224
220.53830.3159-0.52992.05971.59962.51870.24180.17630.0582-0.3822-0.00391.29-0.8143-0.91250.26050.48880.1527-0.0360.6272-0.05860.4612-12.7003-6.930311.9622
233.87490.8413-0.19423.69022.58524.46750.04730.18580.097-0.17520.07870.3897-0.5499-1.18450.09570.34230.092-0.04730.5586-0.02330.3304-8.3245-3.534522.1796
242.63240.1280.11843.78972.88083.67920.1822-0.7652-0.00640.2198-0.28920.05890.2515-0.707-0.17150.2952-0.0546-0.05740.4288-0.01220.1985-0.5969-11.402322.7567
253.4191-0.26240.05612.67571.44124.32860.210.94540.7573-0.9136-0.07860.2798-0.9357-0.62920.03360.67420.1621-0.0060.72450.16620.3891-7.1156-3.64387.0607
265.2621-0.7753-0.5364.54372.77055.75870.0130.02130.1111-0.74070.1922-0.41-0.6196-0.279-0.31770.3455-0.02190.00060.3975-0.01190.23912.5008-7.94312.3798
274.3071-1.09020.86074.27181.15796.3776-0.0599-0.19190.01590.19290.3165-0.4501-0.0084-0.1939-0.12670.2872-0.0653-0.02470.33730.01290.2277-1.5692-15.526211.2598
281.9153-0.0493-0.78992.1422-0.55932.2730.17950.09990.8792-0.6728-0.3446-0.9395-0.4189-0.01460.05310.39850.04650.04760.30450.08620.9996-13.7346-11.565142.42
29-0.00770.19910.17671.7810.67630.7623-0.4604-0.43291.66651.1361-0.2957-0.8741-0.3960.3664-0.72590.5695-0.1846-0.5283-0.1754-0.62321.4796-6.792-11.556758.1983
301.019-0.9444-0.02174.4864-0.18981.5856-0.1483-0.14260.74320.26250.0838-0.0745-0.02210.0020.04770.25020.0264-0.03140.2629-0.05120.5981-16.6639-22.217850.0585
311.6597-1.64450.39922.2805-1.78663.064-0.3457-1.2154-0.06731.39970.5510.82660.431-0.4494-0.09441.10470.19440.20611.24330.07930.6113-19.1089-36.187676.7005
323.3392-2.7324-0.45052.7564-0.89283.0959-0.1842-1.28470.31071.4130.18040.7319-0.2755-0.13520.11550.77680.0480.27960.7445-0.040.5179-20.6274-29.813371.154
333.1238-1.5090.49393.43930.36733.7531-0.551-0.57720.7611.18220.3040.0925-0.5832-0.14330.14360.65720.01890.02490.4349-0.17350.5472-16.5179-23.740763.9107
344.1306-0.8201-0.26641.5784-0.00381.4371-0.8476-1.49780.0511.53620.1661-0.26230.06850.1984-0.05061.17460.277-0.11721.0395-0.25320.5679-9.86-26.925674.1466
351.9954-1.4597-0.62861.9181-1.1443.3543-0.3647-1.2158-0.75721.21140.30370.69660.7164-0.1751-0.07621.03930.270.41850.84740.1380.8134-15.7287-43.682170.4244
364.7344-1.56331.3754.50270.34684.9053-0.3713-0.32330.92350.73030.5037-0.6205-0.06630.56910.09290.53520.0637-0.09160.5871-0.18770.4616-7.3001-32.884464.4507
372.3695-1.9441.04162.2280.31552.632-0.4088-0.86230.55611.33830.3338-0.2926-0.21920.61360.15360.89350.0465-0.20141.1673-0.1790.6049-4.0339-30.233272.8725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 17 )A3 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 26 )A18 - 26
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 33 )A27 - 33
4X-RAY DIFFRACTION4chain 'A' and (resid 34 through 41 )A34 - 41
5X-RAY DIFFRACTION5chain 'A' and (resid 42 through 50 )A42 - 50
6X-RAY DIFFRACTION6chain 'A' and (resid 51 through 60 )A51 - 60
7X-RAY DIFFRACTION7chain 'A' and (resid 61 through 75 )A61 - 75
8X-RAY DIFFRACTION8chain 'A' and (resid 76 through 91 )A76 - 91
9X-RAY DIFFRACTION9chain 'A' and (resid 92 through 99 )A92 - 99
10X-RAY DIFFRACTION10chain 'A' and (resid 100 through 110 )A100 - 110
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 12 )B0 - 12
12X-RAY DIFFRACTION12chain 'B' and (resid 13 through 43 )B13 - 43
13X-RAY DIFFRACTION13chain 'B' and (resid 44 through 65 )B44 - 65
14X-RAY DIFFRACTION14chain 'B' and (resid 66 through 79 )B66 - 79
15X-RAY DIFFRACTION15chain 'B' and (resid 80 through 89 )B80 - 89
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 17 )C3 - 17
17X-RAY DIFFRACTION17chain 'C' and (resid 18 through 26 )C18 - 26
18X-RAY DIFFRACTION18chain 'C' and (resid 27 through 33 )C27 - 33
19X-RAY DIFFRACTION19chain 'C' and (resid 34 through 55 )C34 - 55
20X-RAY DIFFRACTION20chain 'C' and (resid 56 through 86 )C56 - 86
21X-RAY DIFFRACTION21chain 'C' and (resid 87 through 110 )C87 - 110
22X-RAY DIFFRACTION22chain 'D' and (resid 0 through 12 )D0 - 12
23X-RAY DIFFRACTION23chain 'D' and (resid 13 through 33 )D13 - 33
24X-RAY DIFFRACTION24chain 'D' and (resid 34 through 48 )D34 - 48
25X-RAY DIFFRACTION25chain 'D' and (resid 49 through 65 )D49 - 65
26X-RAY DIFFRACTION26chain 'D' and (resid 66 through 79 )D66 - 79
27X-RAY DIFFRACTION27chain 'D' and (resid 80 through 89 )D80 - 89
28X-RAY DIFFRACTION28chain 'E' and (resid 3 through 22 )E3 - 22
29X-RAY DIFFRACTION29chain 'E' and (resid 23 through 56 )E23 - 56
30X-RAY DIFFRACTION30chain 'E' and (resid 57 through 110 )E57 - 110
31X-RAY DIFFRACTION31chain 'F' and (resid 3 through 12 )F3 - 12
32X-RAY DIFFRACTION32chain 'F' and (resid 13 through 23 )F13 - 23
33X-RAY DIFFRACTION33chain 'F' and (resid 24 through 43 )F24 - 43
34X-RAY DIFFRACTION34chain 'F' and (resid 44 through 55 )F44 - 55
35X-RAY DIFFRACTION35chain 'F' and (resid 56 through 65 )F56 - 65
36X-RAY DIFFRACTION36chain 'F' and (resid 66 through 80 )F66 - 80
37X-RAY DIFFRACTION37chain 'F' and (resid 81 through 89 )F81 - 89

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