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- PDB-4f3j: Crystal Structure of Trimeric gC1q Domain of Human C1QTNF5 associ... -

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Basic information

Entry
Database: PDB / ID: 4f3j
TitleCrystal Structure of Trimeric gC1q Domain of Human C1QTNF5 associated with Late-onset Retinal Macular Degeneration
ComponentsComplement C1q tumor necrosis factor-related protein 5
KeywordsSIGNALING PROTEIN / Late-onset Retinal Macular Degeneration / L-ORMD / L-ORD / AMD / age-related macular degeneration / C1QTNF5 / CTRP5 / S163R / Ser163Arg / drusen / retinal deposites / 10-strand jelly-roll fold / MFRP / RPE / ciliary body
Function / homology
Function and homology information


collagen trimer / inner ear development / protein secretion / lateral plasma membrane / bicellular tight junction / transport vesicle / cell projection / apical plasma membrane / extracellular space / identical protein binding / plasma membrane
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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Complement C1q tumor necrosis factor-related protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.337 Å
AuthorsTu, X. / Palczewski, K.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystal structure of the globular domain of C1QTNF5: Implications for late-onset retinal macular degeneration.
Authors: Tu, X. / Palczewski, K.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement C1q tumor necrosis factor-related protein 5


Theoretical massNumber of molelcules
Total (without water)16,4241
Polymers16,4241
Non-polymers00
Water1,62190
1
A: Complement C1q tumor necrosis factor-related protein 5

A: Complement C1q tumor necrosis factor-related protein 5

A: Complement C1q tumor necrosis factor-related protein 5


Theoretical massNumber of molelcules
Total (without water)49,2733
Polymers49,2733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area6750 Å2
ΔGint-43 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.621, 46.621, 138.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-304-

HOH

31A-326-

HOH

41A-346-

HOH

51A-380-

HOH

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Components

#1: Protein Complement C1q tumor necrosis factor-related protein 5


Mass: 16424.301 Da / Num. of mol.: 1 / Fragment: C1QTNF5 gC1q domain, UNP residues 103-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1QTNF5, CTRP5, UNQ303/PRO344 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXJ0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.77 Å3/Da / Density % sol: 30.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Sodium Acetate pH 5.0, 2 M NaCl, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.337→46.277 Å / Num. all: 25129 / Num. obs: 25129 / % possible obs: 98.3 % / Redundancy: 4.8 % / Rsym value: 0.066 / Net I/σ(I): 20.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.337-1.412.50.3242.2839233430.32489.1
1.41-1.495.10.1863.91804735300.18699.8
1.49-1.650.1255.61627432810.125100
1.6-1.725.30.0827.91641731230.082100
1.72-1.8950.0659.41418028300.065100
1.89-2.115.30.0510.71358825480.0599.9
2.11-2.4450.04613.11148422860.046100
2.44-2.995.40.045121027419100.045100
2.99-4.2250.0657.7727814640.065100
4.22-46.2774.90.0826.139578140.082100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.28 Å
Translation2.5 Å46.28 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.3.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.337→46.277 Å / Occupancy max: 1 / Occupancy min: 0.76 / FOM work R set: 0.8959 / SU ML: 0.19 / σ(F): 0.07 / Phase error: 17.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1649 1268 5.11 %RANDOM
Rwork0.1363 ---
obs0.1378 24801 97.42 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.032 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso max: 79.91 Å2 / Biso mean: 26.6506 Å2 / Biso min: 3.11 Å2
Baniso -1Baniso -2Baniso -3
1-4.1914 Å2-0 Å20 Å2
2--4.1914 Å2-0 Å2
3----8.3827 Å2
Refinement stepCycle: LAST / Resolution: 1.337→46.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 0 90 1206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091154
X-RAY DIFFRACTIONf_angle_d1.3731573
X-RAY DIFFRACTIONf_chiral_restr0.095163
X-RAY DIFFRACTIONf_plane_restr0.007205
X-RAY DIFFRACTIONf_dihedral_angle_d13.046397
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.337-1.39040.33971180.2742223234184
1.3904-1.45370.25731330.20922662279598
1.4537-1.53040.21271410.14522644278599
1.5304-1.62620.18451440.123626802824100
1.6262-1.75180.15951170.10012684280199
1.7518-1.92810.15881500.105926772827100
1.9281-2.20710.15851540.11792655280999
2.2071-2.78070.15861530.13612637279099
2.7807-46.2770.15281580.14342671282999

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