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- PDB-5n0k: Rat ceruloplasmin orthorhombic form -

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Basic information

Entry
Database: PDB / ID: 5n0k
TitleRat ceruloplasmin orthorhombic form
ComponentsCeruloplasmin
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Metal ion SLC transporters / glutathione-dependent peroxiredoxin / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / phospholipid-hydroperoxide glutathione peroxidase activity / plasma membrane copper ion transport / Iron uptake and transport / oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / glutathione peroxidase ...Metal ion SLC transporters / glutathione-dependent peroxiredoxin / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / phospholipid-hydroperoxide glutathione peroxidase activity / plasma membrane copper ion transport / Iron uptake and transport / oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / glutathione peroxidase / mammary gland involution / glutathione peroxidase activity / response to copper ion / ferroxidase / ferroxidase activity / intracellular copper ion homeostasis / lactation / response to nutrient / liver development / female pregnancy / lung development / protein-folding chaperone binding / intracellular iron ion homeostasis / oxidoreductase activity / copper ion binding / cell surface / extracellular space / plasma membrane
Similarity search - Function
: / Coagulation factor 5/8-like / 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 ...: / Coagulation factor 5/8-like / 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 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / ferroxidase / Ceruloplasmin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSamygina, V.R. / Sokolov, A.V. / Bourenkov, G. / Vasilyev, V.B.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RFBR15-54-74006 Russian Federation
CitationJournal: Metallomics / Year: 2017
Title: Rat ceruloplasmin: a new labile copper binding site and zinc/copper mosaic.
Authors: Samygina, V.R. / Sokolov, A.V. / Bourenkov, G. / Schneider, T.R. / Anashkin, V.A. / Kozlov, S.O. / Kolmakov, N.N. / Vasilyev, V.B.
History
DepositionFeb 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _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_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)121,69114
Polymers120,8111
Non-polymers87913
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-101 kcal/mol
Surface area38270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.360, 103.810, 172.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Ceruloplasmin / Ceruloplasmin / isoform CRA_a


Mass: 120811.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: G3V7K3, UniProt: P13635*PLUS
#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.: 1
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 , 4 types, 218 molecules

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


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG8000, LITHIUM SULFATE, 0.1M TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 61072 / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.048 / Rrim(I) all: 0.186 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 15.1 % / Rmerge(I) obs: 1.389 / Mean I/σ(I) obs: 2.4 / Num. measured obs: 133202 / Num. unique all: 8809 / Rpim(I) all: 0.367 / Rrim(I) all: 1.437 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4enz

4enz


Resolution: 2.3→14.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.557 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.204 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22627 2996 4.9 %RANDOM
Rwork0.17455 ---
obs0.17706 57741 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.589 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.24 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.3→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8312 0 26 206 8544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198582
X-RAY DIFFRACTIONr_bond_other_d0.0030.027805
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.94211641
X-RAY DIFFRACTIONr_angle_other_deg1.086318039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.87651041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3324.455431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.604151429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4431538
X-RAY DIFFRACTIONr_chiral_restr0.1140.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219786
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022042
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9693.4464143
X-RAY DIFFRACTIONr_mcbond_other1.9683.4464142
X-RAY DIFFRACTIONr_mcangle_it3.3885.1625179
X-RAY DIFFRACTIONr_mcangle_other3.3875.1635180
X-RAY DIFFRACTIONr_scbond_it1.8873.6654439
X-RAY DIFFRACTIONr_scbond_other1.8873.6664440
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2575.4136459
X-RAY DIFFRACTIONr_long_range_B_refined5.96138.4629266
X-RAY DIFFRACTIONr_long_range_B_other5.94138.4279234
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 220 -
Rwork0.276 4145 -
obs--99.98 %
Refinement TLS params.Method: refined / Origin x: 31.191 Å / Origin y: -5.814 Å / Origin z: -24.803 Å
111213212223313233
T0.0301 Å2-0.0031 Å2-0.0026 Å2-0.0162 Å2-0.0148 Å2--0.0531 Å2
L0.4692 °2-0.0827 °20.0264 °2-0.8213 °2-0.038 °2--0.4816 °2
S-0.0134 Å °-0.0156 Å °-0.0177 Å °0.0794 Å °-0.1008 Å °0.1188 Å °-0.0864 Å °-0.0105 Å °0.1142 Å °

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