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- PDB-1h91: The crystal structure of lobster apocrustacyanin A1 using softer ... -

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Basic information

Entry
Database: PDB / ID: 1h91
TitleThe crystal structure of lobster apocrustacyanin A1 using softer X-rays.
ComponentsCRUSTACYANIN A1 SUBUNIT
KeywordsAPOCRUSTACYANIN / SOFTER X-RAYS / XENON / SULPHURS
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-A1 subunit
Similarity search - Component
Biological speciesHOMARUS GAMMARUS (European lobster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsCianci, M. / Rizkallah, P.J. / Olczak, A. / Raftery, J. / Chayen, N.E. / Zagalsky, P.F. / Helliwell, J.R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Lobster Apocrustacyanin A1 Using Softer X-Rays
Authors: Cianci, M. / Rizkallah, P.J. / Olczak, A. / Raftery, J. / Chayen, N.E. / Zagalsky, P.F. / Helliwell, J.R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Apocrustacyanin A1 from the Lobster Carotenoprotein Alpha-Crustacyanin: Crystallization and Initial X- Ray Analysis Involving Softer X-Rays
Authors: Chayen, N.E. / Cianci, M. / Olczak, A. / Raftery, J. / Rizkallah, P.J. / Zagalsky, P.F. / Helliwell, J.R.
History
DepositionFeb 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_data_processing_status / pdbx_database_proc / pdbx_database_status / pdbx_validate_close_contact / struct_biol / struct_conn / struct_conn_type
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_data_processing_status.task_name / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
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_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: CRUSTACYANIN A1 SUBUNIT
B: CRUSTACYANIN A1 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5896
Polymers41,1162
Non-polymers4734
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.650, 80.680, 110.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.05959, 0.89915, 0.43357), (0.90361, -0.23316, 0.35934), (0.42419, 0.37036, -0.82637)
Vector: -18.24337, 22.05606, -1.03611)

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Components

#1: Protein CRUSTACYANIN A1 SUBUNIT / APO A1


Mass: 20558.029 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMARUS GAMMARUS (European lobster) / Tissue: CARAPACE / References: UniProt: P58989*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


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


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AMINO ACID SEQUENCE IS IN GOOD AGREEMENT TO THAT DEPOSITED FOR APO CRUSTACYANIN C1 (SWS ENTRY P80029)

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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: 1.96 Å3/Da / Density % sol: 37.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: HANGING DROP, 18 DEGREES C, OVER RESERVOIR 0.1 M TRIS/HCL, PH 9.0, 5% MPD, 1MM EDTA, 1.9 M AMMONIUM SULPHATE. DROP MADE UP BY MIXING 1:1 PROTEIN SOLUTION (CONTAINING 20 MG/ML A1 SUBUNIT IN 0. ...Details: HANGING DROP, 18 DEGREES C, OVER RESERVOIR 0.1 M TRIS/HCL, PH 9.0, 5% MPD, 1MM EDTA, 1.9 M AMMONIUM SULPHATE. DROP MADE UP BY MIXING 1:1 PROTEIN SOLUTION (CONTAINING 20 MG/ML A1 SUBUNIT IN 0.1 M TRIS-HCL, PH 7.0, 1 MM EDTA) AND OF THE RESERVOIR SOLUTION.
Crystal grow
*PLUS
Temperature: 291 K / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1reservoir
25 %MPD1reservoir
31 mMEDTA1reservoir
41.9 Mammonium sulfate1reservoir
520 mg/mlprotein1drop
60.1 MTris-HCl1drop
71 mMEDTA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.35→100 Å / Num. obs: 73302 / % possible obs: 88.4 % / Redundancy: 8.01 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.6
Reflection shellResolution: 1.35→1.42 Å / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 7.3 / % possible all: 81.8
Reflection
*PLUS
Num. measured all: 330300 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 79.4 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→100 Å / Num. parameters: 21239 / Num. restraintsaints: 25189 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 3137 5 %RANDOM
obs0.1766 -80.1 %-
all-60276 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 30 / Occupancy sum non hydrogen: 3377.2
Refinement stepCycle: LAST / Resolution: 1.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 32 439 3373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0292
X-RAY DIFFRACTIONs_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1766
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.46 Å / Rfactor obs: 0.184

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