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- PDB-5hba: Globular Domain of Zebrafish Complement 1qA protein -

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Basic information

Entry
Database: PDB / ID: 5hba
TitleGlobular Domain of Zebrafish Complement 1qA protein
ComponentsUncharacterized protein
KeywordsIMMUNE SYSTEM / Complement 1q
Function / homology
Function and homology information


Initial triggering of complement / : / Regulation of Complement cascade / complement activation, classical pathway
Similarity search - Function
Complement C1q subcomponent subunit A / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Complement component 1, q subcomponent, A chain
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsXia, C. / Yuan, H. / Chen, R.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31230074 China
the 973 Project of the China Ministry of Science and Technology2013CB835302 China
the open project of State Key Laboratory of Freshwater Ecology and Biotechnology2015FB14 China
CitationJournal: Protein Sci. / Year: 2016
Title: Crystal structure of zebrafish complement 1qA globular domain.
Authors: Yuan, H. / Chen, R. / Tariq, M. / Liu, Y. / Sun, Y. / Xia, C.
History
DepositionDec 31, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6706
Polymers44,3813
Non-polymers2883
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-77 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.347, 85.059, 95.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein / Complement 1q subcomponent subunit A


Mass: 14793.828 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 112-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: c1qa / Production host: Escherichia coli (E. coli) / References: UniProt: F1QFM5
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, PEG 3350 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 26479 / Num. obs: 26479 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/av σ(I): 22.222 / Net I/σ(I): 22.222
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 11.75 / Rsym value: 0.196 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PK6

1pk6


Resolution: 2.05→38.855 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1336 5.06 %
Rwork0.1818 --
obs0.1838 26408 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→38.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3020 0 15 182 3217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073111
X-RAY DIFFRACTIONf_angle_d1.1074207
X-RAY DIFFRACTIONf_dihedral_angle_d12.6161110
X-RAY DIFFRACTIONf_chiral_restr0.078459
X-RAY DIFFRACTIONf_plane_restr0.005534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0466-2.11980.20381280.16752441X-RAY DIFFRACTION98
2.1198-2.20460.22181310.17352481X-RAY DIFFRACTION100
2.2046-2.3050.23871320.17162477X-RAY DIFFRACTION100
2.305-2.42650.2211290.18462470X-RAY DIFFRACTION100
2.4265-2.57850.25461440.19742502X-RAY DIFFRACTION100
2.5785-2.77750.23651270.1862510X-RAY DIFFRACTION100
2.7775-3.05690.23491310.18152515X-RAY DIFFRACTION100
3.0569-3.4990.21871430.17572513X-RAY DIFFRACTION100
3.499-4.40740.18551430.16452526X-RAY DIFFRACTION98
4.4074-38.86210.23591280.20192637X-RAY DIFFRACTION98

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