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- PDB-1kcw: X-RAY CRYSTAL STRUCTURE OF HUMAN CERULOPLASMIN AT 3.0 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1kcw
TitleX-RAY CRYSTAL STRUCTURE OF HUMAN CERULOPLASMIN AT 3.0 ANGSTROMS
ComponentsCERULOPLASMIN
KeywordsOXIDOREDUCTASE / CERULOPLASMIN / MULTI-COPPER OXIDASE / PLASMA PROTEIN
Function / homology
Function and homology information


glutathione-dependent peroxiredoxin / Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) / Defective CP causes aceruloplasminemia (ACERULOP) / phospholipid-hydroperoxide glutathione peroxidase activity / Metal ion SLC transporters / oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / glutathione peroxidase / glutathione peroxidase activity / ferroxidase ...glutathione-dependent peroxiredoxin / Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) / Defective CP causes aceruloplasminemia (ACERULOP) / phospholipid-hydroperoxide glutathione peroxidase activity / Metal ion SLC transporters / oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / glutathione peroxidase / glutathione peroxidase activity / ferroxidase / ferroxidase activity / intracellular copper ion homeostasis / Post-translational protein phosphorylation / Iron uptake and transport / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / protein-folding chaperone binding / iron ion transport / intracellular iron ion homeostasis / blood microparticle / oxidoreductase activity / copper ion binding / endoplasmic reticulum lumen / lysosomal membrane / 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 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 / Ceruloplasmin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsCard, G.L. / Zaitsev, V.N. / Lindley, P.F.
CitationJournal: J.Biol.Inorg.Chem. / Year: 1996
Title: The X-ray structure of human serum ceruloplasmin at 3.1 angstrom: Nature of the copper centres.
Authors: Zaitseva, I. / Zaitsev, V. / Card, G. / Moshkov, K. / Bax, B. / Ralph, A. / Lindley, P.
History
DepositionSep 25, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)121,21413
Polymers120,2311
Non-polymers98312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.920, 213.920, 85.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CERULOPLASMIN


Mass: 120231.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PLASMA / Tissue: PLASMA / 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


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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
Has protein modificationY
Nonpolymer detailsRESIDUES 339 - 346, 475 - 482, 885 - 891 AND 1041 - 1046 AND THE CARBOHYDRATE SIDE CHAINS ATTACHED ...RESIDUES 339 - 346, 475 - 482, 885 - 891 AND 1041 - 1046 AND THE CARBOHYDRATE SIDE CHAINS ATTACHED TO ASN 339 AND ASN 378 ARE MISSING DUE TO BREAKS IN THE ELECTRON DENSITY. ONLY THE FIRST NAG RESIDUE HAS BEEN PLACED FOR ASN 119 AND AND ASN 743.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 70 %
Crystal growpH: 5.65 / Details: pH 5.65
Crystal grow
*PLUS
Temperature: 277 K / pH: 5.45 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128-30 mg/mlhCP1drop
23 %(w/v)PEG200001drop
3250 mM1dropNaCl
4100 mMsodium acetate1drop

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Data collection

DiffractionMean temperature: 276 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 / Wavelength: 0.87, 0.882
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
20.8821
ReflectionResolution: 3→42.64 Å / Num. obs: 44533 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 76.77 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.7 / % possible all: 93.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(ROTAVATA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 3→12 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1336 3 %RANDOM
Rwork0.22 ---
obs0.22 44533 98.5 %-
Displacement parametersBiso mean: 49.8 Å2
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8187 0 38 0 8225
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.04
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.94
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.63
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.1 Å /
Num. reflection% reflection
Rwork3470 -
obs-93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PTOPO.SOL
X-RAY DIFFRACTION3PATOPO.GRAYUM
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.94
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.63

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