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- PDB-6ix1: Structure of 2S albumin seed protein from Dolichos -

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Basic information

Entry
Database: PDB / ID: 6ix1
TitleStructure of 2S albumin seed protein from Dolichos
Components2S Albumin protein
KeywordsPLANT PROTEIN / 2S albumin / beta sheet
Function / homology4 Propeller / Hemopexin / Hemopexin-like domain / Mainly Beta
Function and homology information
Biological speciesDolichos (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsSharma, S.C. / Kumar, A. / Salunke, D.M.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: Sci Rep / Year: 2019
Title: High resolution structural and functional analysis of a hemopexin motif protein from Dolichos.
Authors: Sharma, S.C. / Kumar, A. / Vashisht, S. / Salunke, D.M.
History
DepositionDec 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2S Albumin protein
B: 2S Albumin protein
C: 2S Albumin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,41212
Polymers74,5473
Non-polymers8659
Water11,313628
1
A: 2S Albumin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1374
Polymers24,8491
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-19 kcal/mol
Surface area9250 Å2
MethodPISA
2
B: 2S Albumin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1374
Polymers24,8491
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9230 Å2
MethodPISA
3
C: 2S Albumin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1374
Polymers24,8491
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.158, 65.158, 118.167
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA2 - 2232 - 223
21SERSERLEULEUBB2 - 2232 - 223
12ALAALATHRTHRAA1 - 2251 - 225
22ALAALATHRTHRCC1 - 2251 - 225
13SERSERLEULEUBB2 - 2232 - 223
23SERSERLEULEUCC2 - 2232 - 223

NCS ensembles :
ID
1
2
3

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Components

#1: Protein 2S Albumin protein


Mass: 24849.031 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Dolichos (plant)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.34 % / Description: Rod shaped
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: Sodium acetate trihydrate, Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.693
11K, H, -L20.307
ReflectionResolution: 1.28→31.41 Å / Num. obs: 140457 / % possible obs: 97 % / Redundancy: 2.8 % / CC1/2: 0.986 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.039 / Rrim(I) all: 0.067 / Net I/σ(I): 15.6
Reflection shellResolution: 1.28→1.294 Å / Rmerge(I) obs: 0.432 / Num. unique obs: 13099 / CC1/2: 0.866 / Rpim(I) all: 0.341

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXv1.8.2-1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OYO

3oyo


Resolution: 1.28→31.41 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.38 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.01 / ESU R Free: 0.01 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1698 14272 10.2 %RANDOM
Rwork0.12837 ---
obs0.13262 126208 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.296 Å2
Baniso -1Baniso -2Baniso -3
1--3.41 Å2-0 Å2-0 Å2
2---3.41 Å2-0 Å2
3---6.81 Å2
Refinement stepCycle: 1 / Resolution: 1.28→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5247 0 45 628 5920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0135494
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174980
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.6547469
X-RAY DIFFRACTIONr_angle_other_deg1.6281.57611569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3085690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22621.88266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94315873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8731530
X-RAY DIFFRACTIONr_chiral_restr0.1330.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.026192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021234
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_it2.0551.1052733
X-RAY DIFFRACTIONr_mcbond_other2.0321.1042732
X-RAY DIFFRACTIONr_mcangle_it2.371.6713426
X-RAY DIFFRACTIONr_mcangle_other2.371.6713427
X-RAY DIFFRACTIONr_scbond_it2.7651.2982761
X-RAY DIFFRACTIONr_scbond_other2.7561.2982726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0951.8773988
X-RAY DIFFRACTIONr_long_range_B_refined3.24114.0566175
X-RAY DIFFRACTIONr_long_range_B_other3.06913.6466048
X-RAY DIFFRACTIONr_rigid_bond_restr4.126310474
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A72960.1
12B72960.1
21A70850.13
22C70850.13
31B69120.13
32C69120.13
LS refinement shellResolution: 1.279→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 930 -
Rwork0.255 8666 -
obs--88.93 %

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