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- PDB-4alo: STRUCTURE AND PROPERTIES OF H1 CRUSTACYANIN FROM LOBSTER HOMARUS ... -

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Basic information

Entry
Database: PDB / ID: 4alo
TitleSTRUCTURE AND PROPERTIES OF H1 CRUSTACYANIN FROM LOBSTER HOMARUS AMERICANUS
ComponentsH1 APOCRUSTACYANIN
KeywordsTRANSPORT PROTEIN / CHROMOPHORE BINDING PROTEIN / BATHOCHROMIC SHIFT / ASTAXANTHIN / COLOURATION / RECOMBINANT CAROTENOPROTEINS / CARAPACE
Function / homology
Function and homology information


pigment binding / response to reactive oxygen species / lipid metabolic process / extracellular region / cytoplasm
Similarity search - Function
Invertebrate colouration protein / Lipocalin, ApoD type / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
H1 apocrustacyanin / Crustacyanin-C1 subunit
Similarity search - Component
Biological speciesHOMARUS AMERICANUS (American lobster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsFerrari, M. / Folli, C. / Pincolini, E. / Mcclintock, T.S. / Roessle, M. / Berni, R. / Cianci, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structural Characterization of Recombinant Crustacyanin Subunits from the Lobster Homarus Americanus.
Authors: Ferrari, M. / Folli, C. / Pincolini, E. / Mcclintock, T.S. / Rossle, M. / Berni, R. / Cianci, M.
History
DepositionMar 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: H1 APOCRUSTACYANIN
B: H1 APOCRUSTACYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,52915
Polymers41,3882
Non-polymers1,14013
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-155.1 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.368, 78.423, 105.625
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 H1 APOCRUSTACYANIN


Mass: 20694.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMARUS AMERICANUS (American lobster) / Tissue: CARAPACE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTAGAMI / References: UniProt: P80029, UniProt: J3QW35*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE MATCHED TO CLOSEST UNIPROT ENTRY. THERE IS A GENBANK REFERENCE FOR THIS ENTRY DV771534

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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: 2.06 Å3/Da / Density % sol: 40.45 % / Description: NONE
Crystal growDetails: CRYSTALLIZATION CONDITIONS: H1 PROTEIN SOLUTION AT 10.7 MG/ML IN TRIS-HCL 0.1M, PH 7.0, AND EDTA 1MM WAS USED IN CRYSTALLIZATION EXPERIMENTS. THE BEST CRYSTALS WERE GROWN BY MIXING EQUAL ...Details: CRYSTALLIZATION CONDITIONS: H1 PROTEIN SOLUTION AT 10.7 MG/ML IN TRIS-HCL 0.1M, PH 7.0, AND EDTA 1MM WAS USED IN CRYSTALLIZATION EXPERIMENTS. THE BEST CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF PROTEIN SOLUTION WITH EDTA 1MM, 2.4 M AMMONIUM SULPHATE, 5% V/V 2-METHYL-2,4-PENTANEDIOL (MPD) AND TRIS-HCL PH 8.0 BUFFER. CRYSTALS GREW IN A WEEK TO A SIZE OF 100 BY 30 BY 30 MICROMETERS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.38→20 Å / Num. obs: 13959 / % possible obs: 98.9 % / Observed criterion σ(I): 2.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14
Reflection shellResolution: 2.38→2.46 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.5 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H91

1h91


Resolution: 2.37→62.99 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.609 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.986 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26601 699 5 %RANDOM
Rwork0.22246 ---
obs0.22466 13260 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.481 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.37→62.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 68 98 3084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223059
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.9624166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9165360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89824.4150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50315474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5891512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212348
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.511.51810
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.96922934
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.12731249
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9164.51232
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.375→2.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 50 -
Rwork0.241 939 -
obs--98.12 %

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