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- PDB-5eom: Structure of full-length human MAB21L1 with bound CTP -

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Basic information

Entry
Database: PDB / ID: 5eom
TitleStructure of full-length human MAB21L1 with bound CTP
ComponentsProtein mab-21-like 1
KeywordsTRANSFERASE / Nucleotidyltransferase fold protein
Function / homology
Function and homology information


eye development / camera-type eye development / anatomical structure morphogenesis / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / cell population proliferation / positive regulation of cell population proliferation / GTP binding / ATP binding / nucleus / metal ion binding
Similarity search - Function
Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21
Similarity search - Domain/homology
CITRIC ACID / CYTIDINE-5'-TRIPHOSPHATE / trimethylamine oxide / Putative nucleotidyltransferase MAB21L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
Authorsde Oliveira Mann, C.C. / Witte, G. / Hopfner, K.-P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGRK1721 Germany
CitationJournal: Sci Rep / Year: 2016
Title: Structural and biochemical characterization of the cell fate determining nucleotidyltransferase fold protein MAB21L1.
Authors: de Oliveira Mann, C.C. / Kiefersauer, R. / Witte, G. / Hopfner, K.P.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2May 1, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein mab-21-like 1
B: Protein mab-21-like 1
D: Protein mab-21-like 1
E: Protein mab-21-like 1
F: Protein mab-21-like 1
G: Protein mab-21-like 1
H: Protein mab-21-like 1
I: Protein mab-21-like 1
J: Protein mab-21-like 1
C: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)419,64934
Polymers412,59610
Non-polymers7,05324
Water4,720262
1
A: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0104
Polymers41,2601
Non-polymers7503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9353
Polymers41,2601
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9353
Polymers41,2601
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9353
Polymers41,2601
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0104
Polymers41,2601
Non-polymers7503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
G: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9353
Polymers41,2601
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
H: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1274
Polymers41,2601
Non-polymers8673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
I: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9353
Polymers41,2601
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
J: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7432
Polymers41,2601
Non-polymers4831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
C: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0855
Polymers41,2601
Non-polymers8264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.000, 177.760, 134.940
Angle α, β, γ (deg.)90.00, 97.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein mab-21-like 1


Mass: 41259.617 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAB21L1, CAGR1, Nbla00126 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13394
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9NO
#4: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1M Trisodium citrate 0.1M MES / PH range: 5.5-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 174207 / % possible obs: 99.8 % / Redundancy: 13.9 % / Rsym value: 0.075 / Net I/σ(I): 21.7
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 14 % / Mean I/σ(I) obs: 2.35 / Rsym value: 1.51 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: initial model from Se-SAD

Resolution: 2.55→49.978 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1670 96 %
Rwork0.1992 --
obs0.1995 174180 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→49.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27379 0 440 262 28081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328424
X-RAY DIFFRACTIONf_angle_d0.76538474
X-RAY DIFFRACTIONf_dihedral_angle_d18.21417360
X-RAY DIFFRACTIONf_chiral_restr0.0454213
X-RAY DIFFRACTIONf_plane_restr0.0054883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6250.37031390.320714323X-RAY DIFFRACTION100
2.625-2.70970.33771380.294114275X-RAY DIFFRACTION100
2.7097-2.80660.30361380.273314316X-RAY DIFFRACTION100
2.8066-2.91890.30431390.265614308X-RAY DIFFRACTION100
2.9189-3.05170.31771390.25514353X-RAY DIFFRACTION100
3.0517-3.21260.28841390.240714359X-RAY DIFFRACTION100
3.2126-3.41390.23771390.225814361X-RAY DIFFRACTION100
3.4139-3.67740.26451390.212914364X-RAY DIFFRACTION100
3.6774-4.04730.22541390.197314426X-RAY DIFFRACTION100
4.0473-4.63260.17651400.167314399X-RAY DIFFRACTION100
4.6326-5.83510.22551400.177214444X-RAY DIFFRACTION100
5.8351-49.98720.17541410.164114582X-RAY DIFFRACTION100
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)
12.22180.94331.5511.53982.06983.3628-0.43740.58820.0713-0.37450.14170.0665-1.19380.47420.32730.8168-0.09150.03260.55020.01080.4033169.157657.3561-5.6615
23.80211.04110.62052.429-0.29465.00690.02930.6521-0.3251-0.32660.23940.12770.1156-0.0751-0.23440.6813-0.00230.02150.633-0.02190.378158.990746.0178-21.3612
32.74361.62712.36552.38750.77835.22040.0163-0.20730.1349-0.0973-0.33230.3992-0.2606-0.96890.36270.5274-0.04620.05680.758-0.02460.507153.260945.2349-2.5749
42.42890.12650.77363.87251.52653.70440.0439-0.0259-0.30480.02790.0325-0.05740.2838-0.1107-0.05740.5251-0.10940.01850.41530.03930.3766169.809542.49667.289
53.32683.374-3.83853.7835-5.18687.9417-0.3303-0.1251-0.0824-0.59780.0675-0.00720.46240.39830.3420.8220.02890.04250.4573-0.02480.5251166.93954.291251.454
66.64490.9592-1.03333.662-2.35533.52880.19330.36830.01420.38440.10280.7246-0.4691-0.69-0.24920.74860.05970.01180.518-0.04220.5881145.23341.616667.9634
72.5743-0.73890.12913.7052-2.2933.2268-0.0343-0.17530.28820.35110.09650.2388-0.1878-0.1633-0.06280.6754-0.0488-0.02240.3711-0.03880.5284151.90875.803864.2713
82.83370.1234-0.95343.31770.33.59160.1962-0.15810.30040.4953-0.03750.258-0.42310.1944-0.15870.8027-0.07850.03540.3981-0.0150.5861164.453520.462253.6189
94.8838-3.25631.37655.8169-1.68423.6762-0.6152-0.33371.5120.86430.1834-0.5611-1.1218-0.0530.11931.0247-0.1022-0.03650.4545-0.11560.9238164.002381.933438.1705
102.80530.37461.00362.5470.73252.2579-0.09040.71351.3583-0.178-0.3405-0.8347-1.3647-0.3080.28591.38090.1942-0.02840.87310.36041.7806152.879294.489722.7823
115.3851-1.40072.74942.2837-0.38037.41990.5537-0.15720.0990.2418-0.11670.8446-0.4778-0.8685-0.44310.61960.07890.02980.67080.06480.8982149.17574.018327.3304
123.4756-1.0722-0.57742.2687-1.25117.09210.12080.01870.1453-0.1005-0.12320.0369-0.0697-0.1501-0.00210.5231-0.1368-0.00610.34340.00150.4024167.081966.854228.0192
134.1392-4.232-4.19685.05555.37976.046-0.2432-0.1268-0.39070.28390.09530.19960.16270.07280.10160.568-0.0293-0.03080.47720.01890.5575115.6509-2.903915.4714
146.43870.7374-0.88593.39061.83283.29360.19380.59930.0764-0.25510.3631-0.7493-0.35740.6595-0.52140.9815-0.10720.04430.6077-0.07390.7118135.571-1.7773-3.021
154.82950.66380.25354.49321.66723.0570.008-0.33730.3807-0.31190.1237-0.3692-0.33580.1457-0.11060.4994-0.02140.02840.4254-0.09710.5226125.13522.43768.2305
163.9521-1.9747-3.1633.42683.31243.8479-0.0781-0.09460.4092-0.25450.4406-0.29270.54540.2754-0.45630.7074-0.12340.0460.6377-0.12270.7362128.70376.62088.912
173.6369-0.6652-1.06742.9067-0.07794.03730.1550.08170.321-0.48140.0432-0.3001-0.11380.0084-0.18280.6563-0.0030.04230.4201-0.02670.6684112.289316.214815.3686
184.495-1.4998-2.70612.16781.0762.93340.1222-0.3036-0.186-0.1496-0.01650.1164-0.2861-0.09150.03390.974-0.17650.03480.5632-0.04250.4887154.370151.180673.2234
196.47-1.3482-0.88050.76440.03692.31320.3088-0.45560.51420.2101-0.0595-0.0177-0.66-0.0407-0.33281.1227-0.09880.18240.8058-0.11350.5608150.610865.437683.2293
202.40941.9633-0.22765.8047-1.19198.9232-0.19311.5218-0.7121-0.3907-0.16041.18910.8276-0.48310.04550.7153-0.1682-0.10281.5547-0.130.6903140.356552.312556.2418
212.6159-0.7547-1.08842.6319-0.47182.0003-0.03270.0817-0.3259-0.12240.06920.16250.1222-0.5116-0.05020.7503-0.1384-0.03340.5957-0.08120.3985160.225853.494758.7877
222.4415-3.44632.99249.537-5.79553.9132-0.3438-0.62860.04620.69880.2575-0.0829-0.4644-0.44180.1140.79810.05440.05360.93880.0080.5927108.77969.316665.7922
233.7632-0.337-0.04882.6793-1.09731.6911-0.06-0.0371-0.3799-0.2462-0.0875-0.43310.3732-0.04970.15230.6675-0.0190.0380.60290.13780.5816121.8815-5.883461.8763
243.5996-0.75960.83263.4889-0.59793.1212-0.03630.05310.0105-0.1196-0.1799-0.07620.1601-0.09240.18290.58810.10250.11090.61320.04110.5103110.234312.24548.1305
253.57871.772-1.53881.8188-1.56112.12-0.55180.9611-0.0537-0.67490.3597-0.32290.2589-0.26930.28011.31640.0830.21540.89770.09620.8133122.42247.9619-13.8714
263.36620.3704-1.04463.1302-0.58441.1876-0.09290.033-0.0608-0.3455-0.099-0.43770.14190.2960.19560.5710.13010.01630.60410.15380.597119.402147.98423.2102
272.78530.33353.46011.0606-0.0144.1075-0.0034-0.58880.48530.326-0.30040.386-1.0565-0.68950.22011.212-0.0650.24930.9525-0.16860.7102105.798759.446765.3185
282.8914-1.01542.963.4658-0.09763.28550.1442-0.23920.20291.3007-0.4196-0.1332-0.0801-0.09110.1571.4255-0.34180.07451.1905-0.02240.6273122.883651.802886.1873
292.7981-0.02411.64212.7657-0.66182.46260.5609-0.1329-0.07440.4537-0.510.1427-0.19640.40340.0651.1016-0.13580.05481.1031-0.12610.658118.437449.060474.3609
302.6908-0.07220.67185.6304-1.65843.5958-0.0927-0.0868-0.01510.26530.24910.06850.07920.3308-0.16460.65650.18710.05390.8437-0.10970.5236107.571443.08458.9787
316.7161.4628-0.10682.35053.08394.61780.41650.17330.5151-0.4212-0.59980.9766-0.817-0.60690.19461.06890.2720.18480.79530.02820.6005106.813361.759420.1941
326.0801-0.9452.08340.38740.69344.7589-0.61440.54230.6156-1.44170.4945-0.1754-2.31890.86130.11082.3075-0.28460.54451.0403-0.01091.2129120.400594.288823.2069
332.2435-0.0328-0.07220.0984-0.35610.5654-0.6298-0.66041.34010.05560.0833-0.082-1.31560.3430.29331.9219-0.04930.13091.0017-0.29331.4372121.281592.87335.1738
345.2822-0.60651.41324.0206-0.39133.57920.4153-0.1924-0.5102-0.17670.3142-0.1424-1.03350.7285-0.61481.054-0.15590.21431.0295-0.24611.1956125.272576.464833.9631
351.86133.683.26279.92726.43695.570.9551-0.96760.2735-0.6827-0.6017-0.6285-1.85230.5617-0.32551.1992-0.44060.42741.375-0.43631.1732126.278175.218833.0234
363.5091-0.7203-2.32353.25212.68799.03830.2981-0.3670.44210.0870.0748-0.2357-0.11830.465-0.36360.61510.16110.01060.7036-0.05450.65110.500265.006835.184
372.57992.22222.03673.9943.85664.1629-0.14090.2370.101-0.76140.1568-0.2202-0.61010.29210.06280.6586-0.01860.01770.43240.05050.4388172.518912.72946.2609
386.67651.2734-0.72223.09130.35122.9976-0.06540.1554-0.12940.3011-0.13430.86290.3456-0.23440.19760.76830.02750.09940.3313-0.07510.6473155.8151-9.82885.6269
396.4422-1.8425-1.91284.0131.44712.3987-0.112-0.43570.19690.19180.0210.39380.21570.02030.11210.5095-0.0097-0.01650.4085-0.10420.4263159.9533-1.972910.6004
402.98251.2970.09153.0590.07992.22990.047-0.0523-0.1860.252-0.19460.13550.233-0.08380.12430.5781-0.05150.05550.3162-0.04730.461167.50312.899321.5165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 184 )
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 246 )
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 359 )
5X-RAY DIFFRACTION5chain 'B' and (resid -2 through 48 )
6X-RAY DIFFRACTION6chain 'B' and (resid 49 through 124 )
7X-RAY DIFFRACTION7chain 'B' and (resid 125 through 246 )
8X-RAY DIFFRACTION8chain 'B' and (resid 247 through 359 )
9X-RAY DIFFRACTION9chain 'D' and (resid -1 through 79 )
10X-RAY DIFFRACTION10chain 'D' and (resid 80 through 184 )
11X-RAY DIFFRACTION11chain 'D' and (resid 185 through 246 )
12X-RAY DIFFRACTION12chain 'D' and (resid 247 through 359 )
13X-RAY DIFFRACTION13chain 'E' and (resid 1 through 72 )
14X-RAY DIFFRACTION14chain 'E' and (resid 73 through 141 )
15X-RAY DIFFRACTION15chain 'E' and (resid 142 through 206 )
16X-RAY DIFFRACTION16chain 'E' and (resid 207 through 246 )
17X-RAY DIFFRACTION17chain 'E' and (resid 247 through 359 )
18X-RAY DIFFRACTION18chain 'F' and (resid -2 through 102 )
19X-RAY DIFFRACTION19chain 'F' and (resid 103 through 176 )
20X-RAY DIFFRACTION20chain 'F' and (resid 177 through 206 )
21X-RAY DIFFRACTION21chain 'F' and (resid 207 through 359 )
22X-RAY DIFFRACTION22chain 'G' and (resid -2 through 70 )
23X-RAY DIFFRACTION23chain 'G' and (resid 71 through 230 )
24X-RAY DIFFRACTION24chain 'G' and (resid 231 through 359 )
25X-RAY DIFFRACTION25chain 'H' and (resid -2 through 157 )
26X-RAY DIFFRACTION26chain 'H' and (resid 158 through 359 )
27X-RAY DIFFRACTION27chain 'I' and (resid 1 through 48 )
28X-RAY DIFFRACTION28chain 'I' and (resid 49 through 142 )
29X-RAY DIFFRACTION29chain 'I' and (resid 143 through 246 )
30X-RAY DIFFRACTION30chain 'I' and (resid 247 through 359 )
31X-RAY DIFFRACTION31chain 'J' and (resid -1 through 29 )
32X-RAY DIFFRACTION32chain 'J' and (resid 30 through 65 )
33X-RAY DIFFRACTION33chain 'J' and (resid 66 through 158 )
34X-RAY DIFFRACTION34chain 'J' and (resid 159 through 206 )
35X-RAY DIFFRACTION35chain 'J' and (resid 207 through 246 )
36X-RAY DIFFRACTION36chain 'J' and (resid 247 through 359 )
37X-RAY DIFFRACTION37chain 'C' and (resid -2 through 48 )
38X-RAY DIFFRACTION38chain 'C' and (resid 49 through 141 )
39X-RAY DIFFRACTION39chain 'C' and (resid 142 through 230 )
40X-RAY DIFFRACTION40chain 'C' and (resid 231 through 359 )

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