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- PDB-7tl6: Murine meteorin N-terminal CUB domain -

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Basic information

Entry
Database: PDB / ID: 7tl6
TitleMurine meteorin N-terminal CUB domain
ComponentsMeteorin
KeywordsSIGNALING PROTEIN / meteorin / CUB domain / neurotrophic factor
Function / homology: / radial glial cell differentiation / positive regulation of axonogenesis / axonogenesis / extracellular space / Meteorin
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsQuan, C. / Arndt, J.W. / Pepinsky, B. / Gong, B.J. / Dolnikova, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: To Be Published
Title: Identification and structure determination of stable domains of meteorin and meteorin-like
Authors: Quan, C. / Arndt, J.W. / Pepinsky, R.B. / Gong, B.J. / Dolnikova, J.
History
DepositionJan 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Meteorin
B: Meteorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7803
Polymers29,6842
Non-polymers961
Water905
1
A: Meteorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9382
Polymers14,8421
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Meteorin


Theoretical massNumber of molelcules
Total (without water)14,8421
Polymers14,8421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.508, 48.508, 191.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 5 or (resid 6...
21(chain B and (resid 1 through 47 or resid 54...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASP(chain A and (resid 1 through 5 or (resid 6...AA1 - 51 - 5
12ARGARGARGARG(chain A and (resid 1 through 5 or (resid 6...AA66
13GLYGLYASPASP(chain A and (resid 1 through 5 or (resid 6...AA1 - 1301 - 130
21GLYGLYGLYGLY(chain B and (resid 1 through 47 or resid 54...BB1 - 471 - 47
22ARGARGGLUGLU(chain B and (resid 1 through 47 or resid 54...BB54 - 6354 - 63
23ARGARGARGARG(chain B and (resid 1 through 47 or resid 54...BB6464
24GLYGLYASPASP(chain B and (resid 1 through 47 or resid 54...BB1 - 1301 - 130
25GLYGLYASPASP(chain B and (resid 1 through 47 or resid 54...BB1 - 1301 - 130
26GLYGLYASPASP(chain B and (resid 1 through 47 or resid 54...BB1 - 1301 - 130
27GLYGLYASPASP(chain B and (resid 1 through 47 or resid 54...BB1 - 1301 - 130

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Components

#1: Protein Meteorin / Hypoxia/reoxygenation regulatory factor


Mass: 14841.752 Da / Num. of mol.: 2 / Fragment: CUB domain (UNP residues 22-155)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Metrn, Hyrac / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q8C1Q4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl, pH 8.5, 200 mM lithium sulfate, 31% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.9 Å / Num. obs: 10896 / % possible obs: 99.76 % / Redundancy: 24 % / CC1/2: 0.986 / Rpim(I) all: 0.037 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.29 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1013 / CC1/2: 0.43 / Rpim(I) all: 0.64 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.76 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2919 536 4.92 %
Rwork0.2516 10352 -
obs0.2537 10888 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.82 Å2 / Biso mean: 63.7995 Å2 / Biso min: 29.2 Å2
Refinement stepCycle: final / Resolution: 2.3→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 5 5 1760
Biso mean--72.73 47.18 -
Num. residues----239
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A936X-RAY DIFFRACTION15.054TORSIONAL
12B936X-RAY DIFFRACTION15.054TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.530.35761140.3042506262099
2.53-2.90.32961200.293125352655100
2.9-3.650.2911450.252425642709100
3.65-33.760.27831570.234527472904100
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)
19.44760.3975-1.5524.12590.61964.52560.0381-0.7980.47640.07710.19730.0424-0.5592-0.2336-0.19690.30270.03410.05140.45340.01020.368312.0458-6.074422.7074
24.45143.10351.41012.53971.74581.963-0.13020.5309-0.3547-0.47240.2431-0.45330.06970.2106-0.16180.3030.06810.06750.46450.00990.377519.3224-8.905611.714
38.75370.56890.26534.30850.26435.5606-0.074-0.05790.4522-0.01890.1870.1234-0.17740.0689-0.1290.30070.00930.07550.47640.11730.29117.7226-5.461112.2396
43.92631.86060.68292.00030.16480.96260.233-0.19890.5347-0.0012-0.321-0.5314-0.0728-0.10440.36660.92540.1184-0.07640.49630.0920.66734.2077-0.8562-18.0451
56.2254-0.09292.94461.2757-0.9432.967-0.39990.46781.2261-0.1089-0.3116-0.4737-0.37650.86120.5590.5402-0.0345-0.03170.45980.08310.51348.3578-7.7249-12.938
69.4749-0.3501-0.44236.86141.49264.9446-0.1995-0.8601-0.053-0.9180.483-0.0582-0.31390.3511-0.27730.56250.0234-0.09490.3782-0.02250.49454.2897-16.2565-9.7864
723.71791.8495.52145.36075.5616-1.2691-0.46872.86360.4206-0.6972-1.9331.07031.05352.41871.33850.1314-0.23550.62340.17281.1711-2.201-15.1512-3.8099
81.86231.61681.14213.04910.81214.3060.0167-0.4934-0.5837-0.27740.0735-0.0868-0.4454-0.1569-0.14530.52230.04910.06160.4635-0.00370.41813.8914-14.1999-12.2593
93.03160.03253.83022.43470.25444.843-1.0645-0.9739-0.11550.11040.5764-0.2904-1.27260.19050.37160.4201-0.0074-0.0490.4809-0.03910.478910.0686-6.8455-5.5589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 40 )A1 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 84 )A41 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 130 )A85 - 130
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 21 )B1 - 21
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 62 )B22 - 62
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 84 )B63 - 84
7X-RAY DIFFRACTION7chain 'B' and (resid 85 through 93 )B85 - 93
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 119 )B94 - 119
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 130 )B120 - 130

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