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- PDB-4qql: Crystal structure of C1QL3 in P1 space group -

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Basic information

Entry
Database: PDB / ID: 4qql
TitleCrystal structure of C1QL3 in P1 space group
ComponentsComplement C1q-like protein 3
KeywordsPROTEIN BINDING / Jelly roll fold / C1q / Brain-specific angiogenesis inhibitor G-protein coupled receptor 3 / extracellular
Function / homology
Function and homology information


postsynaptic density assembly / collagen trimer / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synapse organization / synaptic cleft / hippocampal mossy fiber to CA3 synapse / glutamatergic synapse / extracellular region / identical protein binding
Similarity search - Function
: / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls ...: / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Complement C1q-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsRessl, S. / Brunger, A.T.
CitationJournal: Structure / Year: 2015
Title: Structures of C1q-like Proteins Reveal Unique Features among the C1q/TNF Superfamily.
Authors: Ressl, S. / Vu, B.K. / Vivona, S. / Martinelli, D.C. / Sudhof, T.C. / Brunger, A.T.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C1q-like protein 3
B: Complement C1q-like protein 3
C: Complement C1q-like protein 3
D: Complement C1q-like protein 3
E: Complement C1q-like protein 3
F: Complement C1q-like protein 3
G: Complement C1q-like protein 3
H: Complement C1q-like protein 3
I: Complement C1q-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,21033
Polymers136,6279
Non-polymers58324
Water15,961886
1
A: Complement C1q-like protein 3
B: Complement C1q-like protein 3
C: Complement C1q-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,71310
Polymers45,5423
Non-polymers1707
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-70 kcal/mol
Surface area12810 Å2
MethodPISA
2
G: Complement C1q-like protein 3
hetero molecules

D: Complement C1q-like protein 3
F: Complement C1q-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,73711
Polymers45,5423
Non-polymers1948
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-72 kcal/mol
Surface area12800 Å2
MethodPISA
3
E: Complement C1q-like protein 3
H: Complement C1q-like protein 3
I: Complement C1q-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,76112
Polymers45,5423
Non-polymers2199
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-93 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.590, 82.600, 86.200
Angle α, β, γ (deg.)61.44, 84.50, 74.93
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Complement C1q-like protein 3 / C1q and tumor necrosis factor-related protein 13 / C1q/TNF-related protein 13 / CTRP13 / Gliacolin


Mass: 15180.792 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: C1ql3, C1ql, Ctrp13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ESN4
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 886 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate trihydrate, 20% Polyethylene glycol 8,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.39→49.79 Å / Num. obs: 31044 / % possible obs: 65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Rmerge(I) obs: 0.06 / Rsym value: 0.085 / Net I/σ(I): 6.4
Reflection shellHighest resolution: 2.39 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.285 / % possible all: 69.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→46.342 Å / SU ML: 0.29 / σ(F): 1.97 / Phase error: 31.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1554 5.04 %
Rwork0.2238 --
obs0.2256 30852 64.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→46.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9167 0 24 886 10077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049579
X-RAY DIFFRACTIONf_angle_d0.82713008
X-RAY DIFFRACTIONf_dihedral_angle_d11.6093413
X-RAY DIFFRACTIONf_chiral_restr0.0341348
X-RAY DIFFRACTIONf_plane_restr0.0031705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.46710.32051630.27912909X-RAY DIFFRACTION70
2.4671-2.55530.30321520.26442780X-RAY DIFFRACTION68
2.5553-2.65760.32241330.26082754X-RAY DIFFRACTION66
2.6576-2.77860.3591300.25852566X-RAY DIFFRACTION62
2.7786-2.9250.29841540.23722544X-RAY DIFFRACTION62
2.925-3.10820.26151380.23582784X-RAY DIFFRACTION67
3.1082-3.34820.26931470.22072772X-RAY DIFFRACTION67
3.3482-3.6850.21331280.21432509X-RAY DIFFRACTION60
3.685-4.21790.20281490.19922698X-RAY DIFFRACTION66
4.2179-5.31290.18311250.16822560X-RAY DIFFRACTION62
5.3129-46.3510.28451350.21922422X-RAY DIFFRACTION59
Refinement TLS params.Method: refined / Origin x: 27.7418 Å / Origin y: -1.5869 Å / Origin z: 34.7741 Å
111213212223313233
T0.1563 Å20.0141 Å2-0.0114 Å2-0.1957 Å20.0132 Å2--0.1924 Å2
L0.0061 °20.1281 °2-0.0477 °2-0.1649 °20.0693 °2--0.0636 °2
S-0.0117 Å °0.0151 Å °-0.0209 Å °-0.0115 Å °0.0041 Å °0.0107 Å °0.0049 Å °-0.0368 Å °0.0032 Å °
Refinement TLS groupSelection details: all

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