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- PDB-4enz: Structure of human ceruloplasmin at 2.6 A resolution -

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Basic information

Entry
Database: PDB / ID: 4enz
TitleStructure of human ceruloplasmin at 2.6 A resolution
ComponentsCeruloplasmin
KeywordsOXIDOREDUCTASE / plastocyanin-like domains
Function / homology
Function and homology information


Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) / Defective CP causes aceruloplasminemia (ACERULOP) / phospholipid-hydroperoxide glutathione peroxidase activity / Metal ion SLC transporters / cuproxidase / oxidoreductase activity, acting on metal ions, oxygen as acceptor / copper ion transport / glutathione peroxidase activity / ferroxidase / ferroxidase activity ...Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) / Defective CP causes aceruloplasminemia (ACERULOP) / phospholipid-hydroperoxide glutathione peroxidase activity / Metal ion SLC transporters / cuproxidase / oxidoreductase activity, acting on metal ions, oxygen as acceptor / copper ion transport / glutathione peroxidase activity / ferroxidase / ferroxidase activity / intracellular copper ion homeostasis / side of membrane / Iron uptake and transport / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / iron ion transport / protein-folding chaperone binding / intracellular iron ion homeostasis / blood microparticle / oxidoreductase activity / copper ion binding / lysosomal membrane / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal ...: / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / OXYGEN ATOM / OXYGEN MOLECULE / Ceruloplasmin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSamygina, V.R. / Sokolov, A.V. / Bourenkov, G. / Vasilyev, V.B. / Bartunik, H.
CitationJournal: Plos One / Year: 2013
Title: Ceruloplasmin: macromolecular assemblies with iron-containing acute phase proteins.
Authors: Samygina, V.R. / Sokolov, A.V. / Bourenkov, G. / Petoukhov, M.V. / Pulina, M.O. / Zakharova, E.T. / Vasilyev, V.B. / Bartunik, H. / Svergun, D.I.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Ceruloplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,37914
Polymers122,3521
Non-polymers1,02713
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)210.775, 210.775, 84.502
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Ceruloplasmin / / Ferroxidase


Mass: 122351.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00450, ferroxidase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 97 molecules

#3: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 4.43 Å3/Da / Density % sol: 72.23 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 40% MPD, 100 mM sodium chloride, 10 mM calcium chloride, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 26, 2006
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 59714 / Num. obs: 59625 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.7 Å / % possible all: 92.9

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J5W

2j5w


Resolution: 2.6→14.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 20.042 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.306 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23436 3091 4.9 %RANDOM
Rwork0.19897 ---
all0.2168 59714 --
obs0.2007 59625 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.319 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8330 0 45 86 8461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228614
X-RAY DIFFRACTIONr_bond_other_d0.0010.025776
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9411693
X-RAY DIFFRACTIONr_angle_other_deg0.99314027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72251028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36324.305439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.225151402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4081539
X-RAY DIFFRACTIONr_chiral_restr0.1020.21222
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219643
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021808
X-RAY DIFFRACTIONr_mcbond_it0.6691.55118
X-RAY DIFFRACTIONr_mcbond_other0.1141.52085
X-RAY DIFFRACTIONr_mcangle_it1.28628286
X-RAY DIFFRACTIONr_scbond_it1.89933496
X-RAY DIFFRACTIONr_scangle_it3.0754.53406
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 223 -
Rwork0.341 4164 -
obs--92.93 %
Refinement TLS params.Method: refined / Origin x: 8.2971 Å / Origin y: 82.4381 Å / Origin z: 13.4178 Å
111213212223313233
T0.16 Å20.0158 Å20.1029 Å2-0.1125 Å20.0161 Å2--0.1227 Å2
L1.6496 °2-0.6769 °2-0.2302 °2-1.3442 °2-0.2314 °2--1.0223 °2
S-0.1757 Å °-0.1455 Å °-0.3858 Å °0.2226 Å °0.0703 Å °0.2642 Å °0.1462 Å °0.0093 Å °0.1054 Å °

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