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

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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 / homologyMulticopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, type 2 / Multicopper oxidase, type 3 / Ceruloplasmin / Multicopper oxidases, conserved site / Multicopper oxidase / Multicopper oxidase / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site ...Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, type 2 / Multicopper oxidase, type 3 / Ceruloplasmin / Multicopper oxidases, conserved site / Multicopper oxidase / Multicopper oxidase / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Metal ion SLC transporters / Defective CP causes aceruloplasminemia (ACERULOP) / Post-translational protein phosphorylation / Iron uptake and transport / Cupredoxin / copper ion transport / ferroxidase / ferroxidase activity / cellular iron ion homeostasis / lysosomal membrane / iron ion transport / iron ion homeostasis / post-translational protein modification / chaperone binding / copper ion binding / blood microparticle / oxidoreductase activity / endoplasmic reticulum lumen / cellular protein metabolic process / extracellular space / extracellular exosome / extracellular region / plasma membrane / Ceruloplasmin
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 3 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 25, 1996 / Release: Feb 12, 1997
RevisionDateData content typeGroupProviderType
1.0Feb 12, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CERULOPLASMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,21413
Polyers120,2311
Non-polymers98312
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MP 32 2 1

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Components

#1: Protein/peptide CERULOPLASMIN /


Mass: 120231.305 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Genus: Homo / Organ: PLASMA / Tissue: PLASMA / References: UniProt: P00450, ferroxidase
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 15.999 Da / Num. of mol.: 2 / Formula: O / Oxygen
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 / Density percent sol: 7 %
Crystal growpH: 5.65 / Details: pH 5.65
Crystal grow
*PLUS
Temp: 277 K / pH: 5.45 / Method: vapor diffusion, sitting drop
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 / Wavelength: 0.87, 0.882
DetectorType: MARRESEARCH / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Oct 1, 1995
RadiationMonochromator: SI(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
10.871.0
20.8821.0
ReflectionB iso Wilson estimate: 76.77 Å2 / D resolution high: 3 Å / D resolution low: 42.64 Å / Number obs: 44533 / Observed criterion sigma I: 0 / Rmerge I obs: 0.072 / NetI over sigmaI: 7.4 / Redundancy: 7 % / Percent possible obs: 98.5
Reflection shellRmerge I obs: 0.276 / Highest resolution: 3 Å / Lowest resolution: 3.1 Å / MeanI over sigI obs: 2.7 / Redundancy: 5 % / Percent 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
RefineMethod to determine structure: MIR / R Free selection details: RANDOM / Cross valid method: THROUGHOUT
Displacement parametersB iso mean: 49.8 Å2
Least-squares processR factor R free: 0.286 / R factor R work: 0.22 / R factor obs: 0.22 / Highest resolution: 3 Å / Lowest resolution: 12 Å / Number reflection R free: 1336 / Number reflection obs: 44533 / Percent reflection R free: 3 / Percent reflection obs: 98.5
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 12 Å
Number of atoms included #LASTProtein: 8187 / Nucleic acid: 0 / Ligand: 38 / Solvent: 0 / Total: 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
Refine LS shellHighest resolution: 3 Å / Lowest resolution: 3.1 Å / Number reflection R work: 3470 / Percent reflection 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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