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- PDB-2i5r: Structure of small Toprim domain-containing protein from B. stear... -

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Basic information

Entry
Database: PDB / ID: 2i5r
TitleStructure of small Toprim domain-containing protein from B. stearothermophilus in complex with Mg2+
ComponentsToprim domain-containing protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Toprim domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


ribonuclease M5 activity / rRNA processing / metal ion binding
Similarity search - Function
Ribonuclease M5-like, TOPRIM domain / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hypothetical conserved protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRezacova, P. / Borek, D. / Otwinowski, Z. / Joachimiak, A. / Moy, S.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus.
Authors: Rezacova, P. / Borek, D. / Moy, S.F. / Joachimiak, A. / Otwinowski, Z.
History
DepositionAug 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The sequence of this protein is not available in uniprot database at the time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toprim domain-containing protein
B: Toprim domain-containing protein
C: Toprim domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,96214
Polymers41,9733
Non-polymers98911
Water3,801211
1
A: Toprim domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1994
Polymers13,9911
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Toprim domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1994
Polymers13,9911
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Toprim domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5636
Polymers13,9911
Non-polymers5725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.667, 73.031, 114.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 5 - 110 / Label seq-ID: 8 - 113

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Toprim domain-containing protein


Mass: 13990.988 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q5KVJ9*PLUS

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Non-polymers , 5 types, 222 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.86 Å3/Da / Density % sol: 33.85 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES pH 6.5, 26% PEG3350, 18% glycerol, soaking in 25mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorDetector: CCD / Date: Feb 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 38487 / Num. obs: 38256 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 27.7
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3622 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→25.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.641 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20799 1903 5 %RANDOM
Rwork0.17135 ---
obs0.17322 35991 99.58 %-
all-36143 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.241 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.58 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 60 211 3084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223093
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9894202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.71322.53166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3515574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9721546
X-RAY DIFFRACTIONr_chiral_restr0.1550.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022333
X-RAY DIFFRACTIONr_nbd_refined0.2020.21339
X-RAY DIFFRACTIONr_nbtor_refined0.310.22113
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.234
X-RAY DIFFRACTIONr_mcbond_it0.6951.51877
X-RAY DIFFRACTIONr_mcangle_it1.04422951
X-RAY DIFFRACTIONr_scbond_it1.82931357
X-RAY DIFFRACTIONr_scangle_it2.7314.51232
Refine LS restraints NCS

Ens-ID: 1 / Number: 740 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.630.5
2Bmedium positional0.570.5
3Cmedium positional0.730.5
1Amedium thermal0.92
2Bmedium thermal0.872
3Cmedium thermal1.082
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 141 -
Rwork0.197 2602 -
obs--98.95 %
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)
18.53452.0738-1.877411.27726.36217.97570.27880.1280.06060.41260.4322-0.4430.12850.199-0.7111-0.04040.02080.01540.0084-0.0101-0.04145.40951.056-11.222
23.48781.3965-1.94663.9502-2.217410.26680.0974-0.17960.19560.10540.01160.393-0.5113-0.3047-0.109-0.03870.0086-0.01790.0122-0.0016-0.02431.88150.1147.829
38.12281.29411.84669.4253-0.828514.7374-0.22950.20750.5648-0.24280.15030.2989-0.64810.18510.07920.0919-0.0411-0.0533-0.02680.02290.00917.23857.2110.988
412.286910.9597-15.961614.9655-16.895537.6469-0.1877-0.091-0.2698-0.20320.11580.31750.6894-1.22220.0718-0.0526-0.0262-0.04350.03660.01540.0109-1.45445.5046.488
510.24833.7181-7.936711.7964-6.709210.23790.26790.4823-0.6383-0.87160.13411.47710.5723-0.579-0.4020.1166-0.0253-0.2059-0.0131-0.03560.3033-0.76236.581-0.019
63.0588-1.8377-3.18114.48034.20928.5643-0.0157-0.2643-0.05870.31040.3576-0.18070.13950.3239-0.3419-0.0613-0.0016-0.0579-0.0140.0067-0.02057.47642.01512.719
74.4537-1.7382.192415.11598.289914.0601-0.0906-0.0276-0.31010.24370.09080.39870.8122-0.3059-0.00020.0298-0.0323-0.0168-0.01780.05440.03485.3833.94211.033
82.22513.68453.10717.94285.94376.46350.2028-0.0984-0.19550.2437-0.0529-0.22820.38310.0591-0.1499-0.0004-0.0091-0.0429-0.00290.01980.007711.32542.39911.197
91.43052.2906-0.03077.5866-1.4542.2660.0524-0.08340.01690.3185-0.05990.2795-0.0734-0.1390.0075-0.0504-0.0421-0.0322-0.00770.0065-0.039511.63554.31913.417
1015.74091.64893.18329.44530.65278.7561-0.34130.765-0.4455-0.38760.1503-0.2661-0.12760.82740.1910.021-0.07260.0190.0929-0.0362-0.033915.18452.321.763
1134.35090.10357.527115.1661-1.419967.6545-0.3757-0.71450.7589-0.62980.15880.4422-1.26880.84130.21690.0419-0.0522-0.06460.00430.06770.107712.14763.8896.072
1230.874-11.5365-21.588643.648253.718168.07421.2282.5318-1.0074-2.5472-1.65650.5939-2.3089-2.41760.42850.04370.043-0.03870.1527-0.0856-0.027816.25519.555-29.807
133.65420.4324-0.12073.18990.50885.3321-0.0789-0.2033-0.24370.20.0909-0.25130.0460.1346-0.0119-0.07390.02130.0019-0.049-0.0045-0.005418.90521.914-13.27
143.0946-0.7714-3.92036.88249.571619.06530.1894-0.26780.4782-0.14660.4878-0.4524-0.5890.7641-0.6772-0.0322-0.00690.0395-0.0126-0.04980.091323.07236.754-19.994
153.52160.48970.16723.61850.76024.6575-0.03360.1382-0.02550.00050.13530.0278-0.0834-0.404-0.1017-0.08710.0183-0.0038-0.07560.0029-0.019413.85328.657-16.822
167.2101-6.56974.669721.1366-9.239516.8376-0.3738-0.62830.41481.72580.1818-0.2977-1.1834-0.32670.1920.130.0221-0.0117-0.0094-0.05920.021713.69536.823-6.503
172.889-1.9213-1.09878.22061.225510.4101-0.1110.06090.1867-0.039-0.02790.0411-0.2982-0.1160.1389-0.05270.03280.0258-0.02210.01350.030914.03338.633-17.565
183.52041.9322-6.61112.2489-16.775332.95280.2760.15080.24540.12960.17580.55310.3129-0.6296-0.4519-0.0461-0.01310.0378-0.001-0.00310.03797.29928.377-10.958
199.5429-5.1175-1.710212.22143.12235.7168-0.1749-0.42240.05321.0372-0.1754-0.14820.10120.2160.35030.1925-0.02030.00290.03760.02520.04610.06824.124-0.796
202.29360.25080.62136.565-1.229417.3845-0.02240.022-0.2590.3552-0.04860.43860.3978-0.72630.071-0.0479-0.04510.0468-0.0075-0.03810.04165.71918.012-10.451
212.53171.46211.584612.6495-8.440510.6415-0.10190.0551-0.1985-0.4892-0.0774-0.51570.712-0.06520.1794-0.0158-0.01520.0284-0.0016-0.04370.05868.2512.872-15.631
2212.64886.59868.24284.291516.1036169.4362-0.04-0.4796-0.69090.495-0.06020.1319.51190.3620.10020.58270.01380.10190.14940.09110.1415.8648.3320.223
231.313-0.31870.95322.5368-0.98978.74510.04610.13060.0015-0.2215-0.0297-0.05150.08980.215-0.0164-0.12050.0151-0.0083-0.0734-0.0138-0.070918.60725.4322.951
244.02932.75021.16452.25642.6839.73630.03440.0058-0.25-0.09610.2122-0.11040.65990.0621-0.2465-0.02270.0401-0.0281-0.0565-0.028-0.028516.20917.21523.419
252.10233.54584.99948.56098.334312.8669-0.04250.1735-0.1039-0.02640.1798-0.2653-0.00080.4304-0.1374-0.1246-0.0021-0.0039-0.0651-0.0077-0.055822.82728.33726.103
266.02413.4194.34622.07551.056817.851-0.06860.341-0.1882-0.26110.1632-0.07770.26480.194-0.0946-0.0656-0.0181-0.0117-0.0635-0.0021-0.02524.86739.54724.233
272.8813-0.00921.06022.4519-1.88986.6529-0.03550.35740.0257-0.21840.003-0.0326-0.12630.31140.0325-0.0942-0.0048-0.0188-0.0625-0.0138-0.075817.07332.4920.414
281.66840.8025-0.85668.4676-3.38243.2755-0.012-0.09450.04160.2979-0.1529-0.0165-0.1622-0.0090.1649-0.089-0.0051-0.0157-0.0788-0.0143-0.068416.77436.38534.66
291.84792.1973-0.741111.9467-6.00995.2357-0.07640.02780.2240.2374-0.0866-0.1417-0.40050.13050.163-0.0729-0.0014-0.0382-0.0692-0.0031-0.026813.00537.02526.873
303.2221-0.65651.5411.3150.2232.7460.044-0.2106-0.1810.204-0.04330.03470.2167-0.0888-0.0007-0.0395-0.0036-0.003-0.02290.0018-0.031113.65822.0538.809
315.02210.57833.02614.5654-0.94547.79750.0997-0.07640.03040.0748-0.06430.05830.1957-0.1508-0.0354-0.1011-0.0003-0.0163-0.1117-0.0337-0.06127.20418.59429.005
322.5134-0.5733-0.374124.2282-10.69057.0438-0.00620.0486-0.1064-0.4553-0.1918-0.4770.43360.15210.198-0.006-0.0042-0.0232-0.0526-0.0164-0.02410.39213.11922.256
3311.32950.8043-3.331414.2678-5.224713.49450.0799-0.80690.01361.05990.17940.7705-0.5417-0.364-0.25930.020.02090.02370.0599-0.02160.06125.1679.71333.03
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 54 - 8
2X-RAY DIFFRACTION2AA6 - 209 - 23
3X-RAY DIFFRACTION3AA21 - 2624 - 29
4X-RAY DIFFRACTION4AA27 - 3530 - 38
5X-RAY DIFFRACTION5AA36 - 5239 - 55
6X-RAY DIFFRACTION6AA53 - 6456 - 67
7X-RAY DIFFRACTION7AA65 - 7268 - 75
8X-RAY DIFFRACTION8AA73 - 8776 - 90
9X-RAY DIFFRACTION9AA88 - 10191 - 104
10X-RAY DIFFRACTION10AA102 - 108105 - 111
11X-RAY DIFFRACTION11AA109 - 114112 - 117
12X-RAY DIFFRACTION12BB2 - 55 - 8
13X-RAY DIFFRACTION13BB6 - 359 - 38
14X-RAY DIFFRACTION14BB36 - 4839 - 51
15X-RAY DIFFRACTION15BB49 - 6052 - 63
16X-RAY DIFFRACTION16BB61 - 6864 - 71
17X-RAY DIFFRACTION17BB69 - 7772 - 80
18X-RAY DIFFRACTION18BB78 - 8381 - 86
19X-RAY DIFFRACTION19BB84 - 9387 - 96
20X-RAY DIFFRACTION20BB94 - 10497 - 107
21X-RAY DIFFRACTION21BB105 - 113108 - 116
22X-RAY DIFFRACTION22BB114 - 119117 - 122
23X-RAY DIFFRACTION23CC3 - 166 - 19
24X-RAY DIFFRACTION24CC17 - 2620 - 29
25X-RAY DIFFRACTION25CC27 - 3530 - 38
26X-RAY DIFFRACTION26CC36 - 4439 - 47
27X-RAY DIFFRACTION27CC45 - 5848 - 61
28X-RAY DIFFRACTION28CC59 - 7162 - 74
29X-RAY DIFFRACTION29CC72 - 8275 - 85
30X-RAY DIFFRACTION30CC83 - 9386 - 96
31X-RAY DIFFRACTION31CC94 - 10597 - 108
32X-RAY DIFFRACTION32CC106 - 111109 - 114
33X-RAY DIFFRACTION33CC112 - 117115 - 120

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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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