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- PDB-3lp9: Crystal structure of LS24, A Seed Albumin from Lathyrus sativus -

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Basic information

Entry
Database: PDB / ID: 3lp9
TitleCrystal structure of LS24, A Seed Albumin from Lathyrus sativus
ComponentsLS-24
KeywordsPLANT PROTEIN / seed albumin
Function / homology
Function and homology information


nutrient reservoir activity / calcium ion binding / heme binding / cytosol
Similarity search - Function
4 Propeller / Hemopexin / Hemopexin-like domain / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Mainly Beta
Similarity search - Domain/homology
SPERMINE / Albumin-2
Similarity search - Component
Biological speciesLathyrus sativus (chickling vetch)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsGaur, V. / Qureshi, I.A. / Singh, A. / Chanana, V. / Salunke, D.M.
CitationJournal: Plant Physiol. / Year: 2010
Title: Crystal structure and functional insights of hemopexin fold protein from grass pea
Authors: Gaur, V. / Qureshi, I.A. / Singh, A. / Chanana, V. / Salunke, D.M.
History
DepositionFeb 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LS-24
B: LS-24
C: LS-24
D: LS-24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,48417
Polymers102,8884
Non-polymers59613
Water10,178565
1
A: LS-24
C: LS-24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6418
Polymers51,4442
Non-polymers1976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LS-24
D: LS-24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8439
Polymers51,4442
Non-polymers3997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.170, 88.140, 154.530
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 , 1 types, 4 molecules ABCD

#1: Protein
LS-24


Mass: 25721.979 Da / Num. of mol.: 4 / Fragment: Plant Hemopexin domain / Source method: isolated from a natural source / Details: seeds / Source: (natural) Lathyrus sativus (chickling vetch) / References: UniProt: D4AEP7*PLUS

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Non-polymers , 5 types, 578 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE PROTEIN SEQUENCE DATA REPORTED IN THIS ENTRY WILL APPEAR IN THE UNIPROT KNOWLEDGEBASE UNDER THE ...THE PROTEIN SEQUENCE DATA REPORTED IN THIS ENTRY WILL APPEAR IN THE UNIPROT KNOWLEDGEBASE UNDER THE ACCESSION NUMBER P86190. UNK HAS BEEN USED AT POSITIONS 202, 203 AND 206 BECAUSE OF POOR ELECTRON DENSITY FOR SIDE CHAINS IN ALL THE FOUR PROTEIN CHAINS (A,B,C,D). THEY WILL BE CORRECTED ACCORDINGLY IN UNIPROT AT A LATER TIME.

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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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% (w/v) PEG 200000, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 2006 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 54633 / Redundancy: 3.4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 5.2 / Num. measured all: 185883
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.9 / Num. unique all: 8105

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→47.63 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.925 / SU B: 17.713 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 5549 10.2 %RANDOM
Rwork0.24441 ---
obs0.24662 49032 93.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.868 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2--3.76 Å20 Å2
3----2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7220 0 26 565 7811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0227433
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9510052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0235904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73623.889360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8151532
X-RAY DIFFRACTIONr_chiral_restr0.1250.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025812
X-RAY DIFFRACTIONr_nbd_refined0.2440.23566
X-RAY DIFFRACTIONr_nbtor_refined0.3280.25048
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2473
X-RAY DIFFRACTIONr_metal_ion_refined0.0320.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.28
X-RAY DIFFRACTIONr_mcbond_it0.5191.54516
X-RAY DIFFRACTIONr_mcangle_it0.75727268
X-RAY DIFFRACTIONr_scbond_it1.22632999
X-RAY DIFFRACTIONr_scangle_it1.5934.52784
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 438 -
Rwork0.331 3672 -
obs--96.25 %

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