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- PDB-5izn: The crystal structure of 50S ribosomal protein L25 from Vibrio vu... -

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Basic information

Entry
Database: PDB / ID: 5izn
TitleThe crystal structure of 50S ribosomal protein L25 from Vibrio vulnificus CMCP6
Components50S ribosomal protein L25
KeywordsRIBOSOMAL PROTEIN / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


5S rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal Protein L25; Chain P / Ribosomal Protein L25; Chain P / Ribosomal protein L25, short-form / : / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: The crystal structure of 50S ribosomal protein L25 from Vibrio vulnificus CMCP6
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L25
B: 50S ribosomal protein L25
C: 50S ribosomal protein L25
D: 50S ribosomal protein L25
E: 50S ribosomal protein L25
F: 50S ribosomal protein L25
G: 50S ribosomal protein L25
H: 50S ribosomal protein L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,39116
Polymers85,6318
Non-polymers7608
Water1,58588
1
A: 50S ribosomal protein L25
B: 50S ribosomal protein L25
C: 50S ribosomal protein L25
D: 50S ribosomal protein L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2909
Polymers42,8154
Non-polymers4755
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-65 kcal/mol
Surface area19230 Å2
MethodPISA
2
E: 50S ribosomal protein L25
F: 50S ribosomal protein L25
G: 50S ribosomal protein L25
H: 50S ribosomal protein L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1007
Polymers42,8154
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-59 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.451, 58.797, 122.004
Angle α, β, γ (deg.)90.00, 90.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
50S ribosomal protein L25


Mass: 10703.843 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (strain CMCP6) (bacteria)
Strain: CMCP6 / Gene: rplY, VV1_2850 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q8D8W6
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 1.0M NaH2PO4/K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2015 / Details: mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 38178 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 22.446
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 1.3 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000phasing
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.35→34.22 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 1667 4.98 %random
Rwork0.2049 ---
obs0.2072 33500 87.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→34.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5721 0 40 88 5849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025879
X-RAY DIFFRACTIONf_angle_d0.4477946
X-RAY DIFFRACTIONf_dihedral_angle_d11.732180
X-RAY DIFFRACTIONf_chiral_restr0.02880
X-RAY DIFFRACTIONf_plane_restr0.0021043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.41910.3379820.27191364X-RAY DIFFRACTION46
2.4191-2.49720.35231150.2721681X-RAY DIFFRACTION57
2.4972-2.58640.3081090.28292171X-RAY DIFFRACTION72
2.5864-2.68990.30671070.28542589X-RAY DIFFRACTION85
2.6899-2.81230.3381610.27252883X-RAY DIFFRACTION95
2.8123-2.96050.29531490.24832982X-RAY DIFFRACTION99
2.9605-3.14590.2871640.24142983X-RAY DIFFRACTION99
3.1459-3.38860.30631700.22763005X-RAY DIFFRACTION99
3.3886-3.72920.24111280.19473044X-RAY DIFFRACTION99
3.7292-4.26790.21171520.17033016X-RAY DIFFRACTION100
4.2679-5.37380.18691440.14843080X-RAY DIFFRACTION100
5.3738-34.22370.2051860.17213035X-RAY DIFFRACTION97
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)
19.52843.3552-5.75233.186-1.53527.74310.72811.52090.4993-1.7782-0.618-0.91170.15771.77690.13670.4118-0.09110.08720.5450.01350.270548.041838.85747.1704
25.77521.9015-0.83118.98974.85043.66150.2536-0.3518-0.34950.7121-0.21210.1260.61880.3901-0.02220.24210.08480.00230.21230.07080.319250.613735.080866.7302
32.5286-0.5489-0.70955.7405-0.39213.9053-0.47050.12310.1205-0.79960.24710.14760.10270.26160.10320.1366-0.03510.0130.11270.04950.314544.210835.935456.1578
43.4015-3.05741.63472.9617-0.24938.2877-0.22970.0146-0.0994-0.43140.03320.06270.28960.24030.20710.2001-0.00960.01220.1609-0.01770.300140.566537.806248.6696
51.9807-0.7966-3.2771.80210.42865.95790.44170.7403-1.8113-0.27460.1224-0.13080.9824-0.7037-0.60010.3458-0.0617-0.1260.352-0.10540.656335.872749.092563.9583
65.39051.2637-2.17285.482.14374.5944-0.3769-0.26050.1083-0.3710.23610.3162-1.21680.742-0.11190.33410.0074-0.12110.241-0.10050.297146.726262.153580.3374
78.9465-3.8187-3.02392.73610.0093.89170.26560.18071.3211-0.23-0.21490.3832-1.6407-1.6144-0.65720.60440.1938-0.21570.3657-0.15820.740534.492167.331877.7265
85.8905-0.3662.2338.69264.46084.78310.3375-0.6732-0.37930.84830.17290.22650.535-0.197-0.42670.1821-0.09410.04780.22130.01360.341637.238547.346282.0224
93.26140.32130.58923.91560.2413.1214-0.4153-0.30650.6695-0.1261-0.01420.302-0.5971-0.11050.27560.2081-0.019-0.04770.1355-0.09330.322541.073260.874876.861
101.6908-1.6875-1.72062.98292.41255.6020.1162-0.10990.8297-0.0507-0.16050.0167-1.4206-0.0876-0.15170.46150.0026-0.21770.1222-0.07840.811841.253467.771278.4169
115.0650.1546-0.32985.66091.30164.09590.034-0.79911.3318-0.0531-0.23850.2189-0.83970.05920.22040.42850.0122-0.17440.2891-0.12010.368244.090166.35881.4867
124.45982.38873.61327.88815.65928.6636-0.24160.2388-0.4266-0.2784-0.10150.1862-0.47410.08720.18210.03340.0595-0.03550.2383-0.07270.309747.178750.884866.571
134.39153.41913.85873.99564.15144.41510.1665-0.031-0.04350.1132-0.28540.30960.786-0.23830.19180.3062-0.05580.05920.1644-0.02170.232238.509633.041854.1818
142.5215-0.37672.37053.3054-1.63484.87550.466-0.5425-0.72080.22580.2178-0.02011.0191-0.1489-1.23890.4310.312-0.08420.57570.29870.274262.17138.386283.6457
154.90891.5966-3.60897.5883-3.69626.2140.15540.50110.02440.05320.0263-0.8266-0.67360.4368-0.23370.197-0.0603-0.02620.56860.03350.285969.65255.921377.3642
164.3182-2.2873-0.21925.33491.40962.2246-0.1704-0.65130.2050.32920.22-0.06450.43840.23830.02630.11560.0412-0.02550.33120.0680.046457.57551.696380.355
173.56120.6005-0.53254.61921.46864.3586-0.128-0.4466-0.31110.5392-0.1352-0.86811.01090.44910.02620.31170.129-0.02530.42420.14610.202665.869243.191277.4506
187.13470.70041.19347.9591-0.27487.6689-0.1272-0.0406-1.9387-0.4439-0.36290.02671.873-0.26240.10220.5807-0.0860.02050.2608-0.0010.41756.984735.413574.6082
196.29721.10390.25195.50520.25384.36890.337-0.9805-0.17420.35440.044-0.06420.5836-0.12940.14470.1375-0.0724-0.05950.49950.15990.221959.463844.431586.7632
204.12970.5855-1.30414.3403-1.3698.83960.0508-0.3209-0.1145-0.0723-0.19320.15970.4189-0.4414-0.14060.2232-0.0434-0.01780.29230.22870.147755.483845.394479.1608
213.41530.0749-1.33851.9153-0.6017.4260.018-0.1065-0.3473-0.3154-0.0292-0.16721.01070.5927-0.00610.24280.0566-0.01120.28220.05610.234161.970847.387370.5104
226.37140.66314.83384.5551.20554.02760.5718-1.0444-0.43480.4628-0.27880.10020.5738-1.12-0.25320.1969-0.0929-0.05890.36480.06470.358723.930428.746770.5192
230.7454-0.05361.11042.32361.03444.1666-0.0333-0.59040.1199-0.2592-0.32260.29890.0639-1.11190.09680.1451-0.101-0.00490.3470.00090.349919.117634.165366.9632
245.26910.7108-1.74482.07671.01254.0736-0.1037-0.7504-0.37370.3164-0.44160.04060.4762-0.29760.17860.0545-0.17760.04430.25450.00980.324727.125133.08672.6009
256.67360.44391.48628.91562.05291.31220.1689-0.88160.22371.085-0.0711-0.87310.563-0.43650.0450.3249-0.0958-0.04740.30560.10040.236331.89634.645279.5381
265.09020.7522-2.10468.45680.22840.96440.4798-0.6013-0.4757-0.9102-0.3109-0.14090.3752-0.0622-0.04860.3177-0.1168-0.19570.16850.0860.334733.704834.1872.6635
276.5853-0.89831.27853.35930.46814.6746-0.1391-0.42121.22760.2659-0.3345-0.1657-0.5497-0.57530.30480.2353-0.0238-0.01540.1342-0.00330.49825.376941.861270.8643
285.4925-1.1040.64691.1286-0.29260.108-0.08220.17180.29780.1893-0.3621-0.35660.5487-0.38430.21951.0682-0.12060.00350.71150.29140.37578.135719.8731121.6171
294.75210.6133-1.5532.33851.71683.44270.03690.0758-0.38570.21020.157-0.30730.5823-0.6594-0.04050.8263-0.11240.01020.5760.14050.229413.682517.537117.2443
306.4587-1.5693-0.72682.60722.63763.3661-0.25930.1715-1.22190.8147-0.33280.0340.6948-1.16980.0871.0566-0.49680.18610.9712-0.02370.56928.23229.7078116.4124
315.02456.00072.71757.53362.9381.69540.33370.54250.18040.7560.39890.1875-0.0892-0.1956-0.67020.9947-0.21360.06590.6405-0.01530.452228.89632.7872110.6167
321.0351.09391.37033.24361.31052.2823-1.14411.0980.1823-0.43280.45880.36840.083-0.05170.41640.8365-0.30360.04690.86620.01040.587326.709840.6501104.3239
332.52911.18550.79852.64270.59650.2747-0.07020.9884-0.13540.13820.1390.09-0.2601-0.1313-0.20991.1141-0.53710.12870.8706-0.17020.30729.281140.125107.8562
343.19510.92360.25715.86660.584.2634-0.44620.4864-0.47050.21880.0780.08510.2193-0.18040.21240.7932-0.28120.12850.6414-0.05010.460134.673940.4517108.5667
353.17580.13533.25273.1021-1.60678.72390.33880.4306-0.8885-0.2775-0.1589-0.32060.75750.439-0.19540.9625-0.18160.0790.4967-0.10820.523641.808735.669110.008
366.3834-0.3591.02429.3051-6.28444.3442-0.32930.0947-0.4155-0.37890.1730.31110.7162-0.56480.32270.8243-0.22020.18090.5424-0.10210.421940.537443.1033110.2144
372.96852.25731.69449.10681.72091.2902-0.8327-0.22610.4056-0.24921.7706-2.4763-0.88662.2704-0.97461.23150.0017-0.02170.9605-0.08660.776531.067127.2168119.427
383.52021.22933.10044.2452.65363.7902-0.6860.2415-0.663-0.60420.6445-0.04090.0039-0.8040.09910.7793-0.20550.03170.59220.13350.413512.625317.1012112.5832
399.93812.66146.58115.3078-1.39446.52690.0062-0.73071.63420.3735-1.04761.0087-1.0655-1.09590.34750.45940.05120.1750.565-0.1140.3282.077333.565795.8243
407.8372.06973.7263.9624-2.87846.16710.59250.8183-1.5767-0.4116-0.7241-0.7862-0.00150.48350.00370.55040.2830.10661.02480.23750.558910.352119.068188.0316
412.96681.62910.16785.1149-3.53868.32820.2903-0.13810.33980.7419-0.24660.1696-0.7747-0.29220.42850.4484-0.1224-0.14360.77280.24770.10597.768628.438196.6317
422.6695-2.12721.23152.39181.0886.69460.4478-1.42931.61341.0474-0.0592-0.0825-1.74431.0394-0.32711.186-0.320.02210.9974-0.26550.53698.026936.9072100.1989
434.772-0.2363-0.77944.91570.4029.10240.1359-1.26790.37740.8235-0.66650.1215-0.97280.66560.50590.8933-0.2241-0.00410.7707-0.00270.32368.144730.5248102.8736
448.2988-0.0346-3.46374.4894-1.77466.91160.5770.05690.39390.3388-0.4253-0.5636-0.61470.3570.2030.5119-0.149-0.08190.720.08390.254216.158429.293395.6041
454.54740.2074-4.51524.9019-0.17825.46030.1544-1.42060.52121.1104-0.18220.0907-1.26730.70890.15131.08140.01-0.0490.7388-0.17830.525526.126145.0731135.3028
464.97932.82080.66136.3229-0.19274.68990.456-0.83990.92510.36230.29740.9369-0.6231-0.3079-0.42360.76890.08260.17490.5061-0.15030.482219.070740.9448128.9165
476.21710.62230.58667.35970.18918.4028-0.1903-0.390.84690.58770.96920.6815-0.6876-0.0805-0.74980.51390.06310.10450.3987-0.02990.626119.017239.5902127.3797
487.73070.6935-0.07842.9751-2.94432.96280.20340.02991.16220.1807-0.09870.1889-0.31520.6457-0.64830.59640.0090.08380.4136-0.04030.448122.336839.1879125.1281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 49 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 75 )
5X-RAY DIFFRACTION5chain 'A' and (resid 76 through 85 )
6X-RAY DIFFRACTION6chain 'A' and (resid 86 through 92 )
7X-RAY DIFFRACTION7chain 'B' and (resid -1 through 5 )
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 55 )
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 63 )
11X-RAY DIFFRACTION11chain 'B' and (resid 64 through 75 )
12X-RAY DIFFRACTION12chain 'B' and (resid 76 through 85 )
13X-RAY DIFFRACTION13chain 'B' and (resid 86 through 92 )
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 4 )
15X-RAY DIFFRACTION15chain 'C' and (resid 5 through 22 )
16X-RAY DIFFRACTION16chain 'C' and (resid 23 through 36 )
17X-RAY DIFFRACTION17chain 'C' and (resid 37 through 49 )
18X-RAY DIFFRACTION18chain 'C' and (resid 50 through 58 )
19X-RAY DIFFRACTION19chain 'C' and (resid 59 through 65 )
20X-RAY DIFFRACTION20chain 'C' and (resid 66 through 76 )
21X-RAY DIFFRACTION21chain 'C' and (resid 77 through 92 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 12 )
23X-RAY DIFFRACTION23chain 'D' and (resid 13 through 30 )
24X-RAY DIFFRACTION24chain 'D' and (resid 31 through 49 )
25X-RAY DIFFRACTION25chain 'D' and (resid 50 through 65 )
26X-RAY DIFFRACTION26chain 'D' and (resid 66 through 76 )
27X-RAY DIFFRACTION27chain 'D' and (resid 77 through 92 )
28X-RAY DIFFRACTION28chain 'E' and (resid 0 through 14 )
29X-RAY DIFFRACTION29chain 'E' and (resid 15 through 58 )
30X-RAY DIFFRACTION30chain 'E' and (resid 59 through 75 )
31X-RAY DIFFRACTION31chain 'E' and (resid 76 through 92 )
32X-RAY DIFFRACTION32chain 'F' and (resid 1 through 22 )
33X-RAY DIFFRACTION33chain 'F' and (resid 23 through 29 )
34X-RAY DIFFRACTION34chain 'F' and (resid 30 through 49 )
35X-RAY DIFFRACTION35chain 'F' and (resid 50 through 63 )
36X-RAY DIFFRACTION36chain 'F' and (resid 64 through 75 )
37X-RAY DIFFRACTION37chain 'F' and (resid 76 through 81 )
38X-RAY DIFFRACTION38chain 'F' and (resid 82 through 92 )
39X-RAY DIFFRACTION39chain 'G' and (resid 0 through 7 )
40X-RAY DIFFRACTION40chain 'G' and (resid 8 through 22 )
41X-RAY DIFFRACTION41chain 'G' and (resid 23 through 49 )
42X-RAY DIFFRACTION42chain 'G' and (resid 50 through 65 )
43X-RAY DIFFRACTION43chain 'G' and (resid 66 through 76 )
44X-RAY DIFFRACTION44chain 'G' and (resid 77 through 92 )
45X-RAY DIFFRACTION45chain 'H' and (resid 1 through 21 )
46X-RAY DIFFRACTION46chain 'H' and (resid 22 through 56 )
47X-RAY DIFFRACTION47chain 'H' and (resid 57 through 83 )
48X-RAY DIFFRACTION48chain 'H' and (resid 84 through 92 )

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