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- PDB-1s2p: The structure and refinement of apocrustacyanin C2 to 1.3A resolu... -

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Basic information

Entry
Database: PDB / ID: 1s2p
TitleThe structure and refinement of apocrustacyanin C2 to 1.3A resolution and the search for differences between this protein and the homologous apoproteins A1 and C1
ComponentsCrustacyanin C2 subunit
KeywordsPROTEIN BINDING / Apocrustacyanin / X-ray refinement / post-translational modifications
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
Crustacyanin-C1 subunit
Similarity search - Component
Biological speciesHomarus gammarus (European lobster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / not applicable / Resolution: 1.3 Å
AuthorsHabash, J. / Helliwell, J.R. / Raftery, J. / Cianci, M. / Rizkallah, P.J. / Chayen, N.E. / NNeji, G.A. / Zakalsky, P.F.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: The structure and refinement of apocrustacyanin C2 to 1.3 A resolution and the search for differences between this protein and the homologous apoproteins A1 and C1.
Authors: Habash, J. / Helliwell, J.R. / Raftery, J. / Cianci, M. / Rizkallah, P.J. / Chayen, N.E. / Nneji, G.A. / Zagalsky, P.F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of lobster apocrustacyanin A1 using softer X-rays
History
DepositionJan 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_residues / Item: _diffrn_source.type
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crustacyanin C2 subunit
B: Crustacyanin C2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8036
Polymers41,3742
Non-polymers4284
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-73 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.148, 79.846, 110.263
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 Crustacyanin C2 subunit


Mass: 20687.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homarus gammarus (European lobster) / References: UniProt: P80029
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 2.3M ammonium sulphate, 5%MPD, 0.1M Tris HCl, pH 7, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Type: SRS / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→45.2 Å / Num. all: 87664 / Num. obs: 87664 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0.4 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.4
Reflection shellResolution: 1.3→1.37 Å / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 0.8 / Num. unique all: 13016 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: not applicable
Starting model: PDB entry 1H91

1h91


Resolution: 1.3→45.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.091 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21473 4296 5 %RANDOM
Rwork0.18914 ---
all0.19044 87664 --
obs0.19044 87664 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.71 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 10 483 3411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213026
X-RAY DIFFRACTIONr_bond_other_d0.0010.022548
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9434113
X-RAY DIFFRACTIONr_angle_other_deg2.29235977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2073358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37415508
X-RAY DIFFRACTIONr_chiral_restr0.1140.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023372
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02648
X-RAY DIFFRACTIONr_nbd_refined0.2110.3526
X-RAY DIFFRACTIONr_nbd_other0.20.32383
X-RAY DIFFRACTIONr_nbtor_other0.3270.55
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.5382
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.328
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4630.537
X-RAY DIFFRACTIONr_mcbond_it0.9941.51798
X-RAY DIFFRACTIONr_mcangle_it1.57122915
X-RAY DIFFRACTIONr_scbond_it2.11431228
X-RAY DIFFRACTIONr_scangle_it3.1224.51198
X-RAY DIFFRACTIONr_rigid_bond_restr1.13323026
X-RAY DIFFRACTIONr_sphericity_free2.1932467
X-RAY DIFFRACTIONr_sphericity_bonded1.7722944
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.425 305
Rwork0.37 5510
obs-5510

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