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- PDB-5eog: Structure of full-length human MAB21L1 -

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Basic information

Entry
Database: PDB / ID: 5eog
TitleStructure of full-length human MAB21L1
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 / metal ion binding / nucleus
Similarity search - Function
Mab-21-like, nucleotidyltransferase domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21
Similarity search - Domain/homology
CITRIC ACID / Putative nucleotidyltransferase MAB21L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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

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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
F: Protein mab-21-like 1
C: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,25910
Polymers206,2985
Non-polymers9615
Water724
1
A: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4522
Polymers41,2601
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4522
Polymers41,2601
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4522
Polymers41,2601
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4522
Polymers41,2601
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Protein mab-21-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4522
Polymers41,2601
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.100, 176.990, 115.110
Angle α, β, γ (deg.)90.00, 126.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein mab-21-like 1


Mass: 41259.617 Da / Num. of mol.: 5
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.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.59 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1M Trisodium citrate 0.1M MES / PH range: 5.5

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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: 3.05→50 Å / Num. obs: 50759 / % possible obs: 98.8 % / Redundancy: 7 % / Rsym value: 0.044 / Net I/σ(I): 22.51
Reflection shellResolution: 3.05→3.13 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 1.157 / % possible all: 98.1

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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: 3.05→48.592 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2795 2568 5.06 %
Rwork0.2226 --
obs0.2254 50741 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→48.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13117 0 65 4 13186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913441
X-RAY DIFFRACTIONf_angle_d1.20118147
X-RAY DIFFRACTIONf_dihedral_angle_d23.5925103
X-RAY DIFFRACTIONf_chiral_restr0.061994
X-RAY DIFFRACTIONf_plane_restr0.0072321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.10870.43261260.4052635X-RAY DIFFRACTION98
3.1087-3.17210.41861380.35852626X-RAY DIFFRACTION98
3.1721-3.24110.40161340.33282672X-RAY DIFFRACTION99
3.2411-3.31650.37011370.29422683X-RAY DIFFRACTION99
3.3165-3.39940.34391370.28052674X-RAY DIFFRACTION99
3.3994-3.49130.35951560.2772648X-RAY DIFFRACTION99
3.4913-3.5940.33251230.26952710X-RAY DIFFRACTION99
3.594-3.70990.29521510.24382630X-RAY DIFFRACTION99
3.7099-3.84250.32291690.23692646X-RAY DIFFRACTION99
3.8425-3.99620.28671710.23822638X-RAY DIFFRACTION99
3.9962-4.1780.29231420.21022683X-RAY DIFFRACTION100
4.178-4.39820.23411300.19662688X-RAY DIFFRACTION99
4.3982-4.67350.2381310.18132709X-RAY DIFFRACTION100
4.6735-5.0340.2511530.17162673X-RAY DIFFRACTION100
5.034-5.540.25831410.21642718X-RAY DIFFRACTION100
5.54-6.34010.36791400.24232689X-RAY DIFFRACTION100
6.3401-7.98220.26261510.25252706X-RAY DIFFRACTION100
7.9822-48.59810.24281380.1962745X-RAY DIFFRACTION99
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)
15.14550.0081.5981.21310.40143.2128-0.657-0.45970.3916-0.4430.06640.4622-0.7687-1.25750.48721.24310.0632-0.29151.52470.13981.1934186.612253.428-89.6602
21.9641-1.04951.3522.4044-2.69194.5003-0.1326-0.15070.05010.60570.160.0219-0.63520.00460.00711.2642-0.0682-0.13040.8048-0.00571.1769232.153912.1889-45.8609
35.1046-2.82-0.87664.54062.17994.1756-0.4163-0.5941.122-0.06490.1093-0.2154-0.9038-0.37170.22061.14690.1331-0.22180.86520.01131.0855213.619878.8607-65.3658
41.00580.34630.53282.35941.64456.80470.1123-0.27280.08660.8097-0.1597-0.21150.6114-0.30380.02341.1231-0.2813-0.15610.98050.15381.0943240.39356.6017-38.753
54.01392.677-0.23713.87520.66171.35050.00570.41640.06970.0428-0.08010.16230.2898-0.09360.04471.1807-0.1542-0.18850.88450.10070.8887197.24348.3259-78.9725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 359)
2X-RAY DIFFRACTION2(chain 'B' and resid -2 through 359)
3X-RAY DIFFRACTION3(chain 'D' and resid -1 through 359)
4X-RAY DIFFRACTION4(chain 'F' and resid -2 through 359)
5X-RAY DIFFRACTION5(chain 'C' and resid -1 through 359)

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