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- PDB-1hzf: C4ADG FRAGMENT OF HUMAN COMPLEMENT FACTOR C4A -

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Basic information

Entry
Database: PDB / ID: 1hzf
TitleC4ADG FRAGMENT OF HUMAN COMPLEMENT FACTOR C4A
ComponentsCOMPLEMENT FACTOR C4A
KeywordsIMMUNE SYSTEM / alpha-alpha 6 barrel
Function / homology
Function and homology information


: / detection of molecule of bacterial origin / opsonization / complement component C1q complex binding / complement binding / positive regulation of apoptotic cell clearance / regulation of complement activation / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity ...: / detection of molecule of bacterial origin / opsonization / complement component C1q complex binding / complement binding / positive regulation of apoptotic cell clearance / regulation of complement activation / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / carbohydrate binding / blood microparticle / inflammatory response / endoplasmic reticulum lumen / axon / innate immune response / neuronal cell body / synapse / dendrite / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Complement component C4-A / : / Complement C4, MG1 domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system ...Complement component C4-A / : / Complement C4, MG1 domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Glycosyltransferase - #20 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin-like fold / Mainly Alpha
Similarity search - Domain/homology
Complement C4-B / Complement C4-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Authorsvan den Elsen, J.M.H. / Martin, A. / Wong, V. / Clemenza, L. / Rose, D.R. / Isenman, D.E.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: X-ray crystal structure of the C4d fragment of human complement component C4.
Authors: van den Elsen, J.M. / Martin, A. / Wong, V. / Clemenza, L. / Rose, D.R. / Isenman, D.E.
History
DepositionJan 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMPLEMENT FACTOR C4A


Theoretical massNumber of molelcules
Total (without water)39,5891
Polymers39,5891
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.510, 71.430, 85.740
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 COMPLEMENT FACTOR C4A


Mass: 39589.055 Da / Num. of mol.: 1 / Fragment: C4ADG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C4HU / Plasmid: PSVC4A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P01028, UniProt: P0C0L4*PLUS, classical-complement-pathway C3/C5 convertase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, TRIS, magnesium chloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
128 %PEG40001reservoir
20.1 MTris-HCl1reservoirpH7.5
30.2 M1reservoirMgCl2
45 mMdithiothreitol1reservoir
510 mg/mlprotein1drop
610 mMTris-HCl1droppH8.5
710 mM1dropNaCl
82 mMEDTA1drop
95 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 1999 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→26.84 Å / Num. all: 15682 / Num. obs: 15703 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 23.5 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 31 / Limit k min: 0 / Limit l max: 37 / Limit l min: 0 / Observed criterion F max: 729503.73 / Observed criterion F min: 0.89 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2 / Num. unique all: 1057 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. measured all: 43751 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 99.4 % / Num. unique obs: 1057 / Num. measured obs: 2898 / Rmerge(I) obs: 0.511

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3D

1c3d


Resolution: 2.3→26.84 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 724 4.9 %RANDOM
Rwork0.215 ---
all-15992 --
obs-14872 93 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 43.5389 Å2 / ksol: 0.348081 e/Å3
Displacement parametersBiso max: 83.96 Å2 / Biso mean: 41.62 Å2 / Biso min: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1-4.62 Å20 Å20 Å2
2---5 Å20 Å2
3---0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→26.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 0 77 2363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg19.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.82
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.40.32773.90.2916340.0331973171186.7
2.4-2.530.297804.10.27917060.0311964178690.9
2.53-2.690.304944.80.2717290.0281970182392.5
2.69-2.90.2511045.30.26117610.0261970186594.7
2.9-3.190.263914.60.24618020.0261987189395.3
3.19-3.650.214904.50.20218380.0211995192896.6
3.65-4.590.207974.80.17618420.0182019193996
4.59-26.840.202914.30.18618360.0192126192790.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 500 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.04
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / Rfactor Rwork: 0.29

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