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- PDB-4yeh: Crystal structure of Mg2+ ion containing hemopexin fold from Kabu... -

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Basic information

Entry
Database: PDB / ID: 4yeh
TitleCrystal structure of Mg2+ ion containing hemopexin fold from Kabuli chana (chickpea white) at 2.45A resolution reveals a structural basis of metal ion transport
ComponentsLectin
KeywordsPLANT PROTEIN
Function / homology
Function and homology information


4 Propeller / Hemopexin / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Mainly Beta
Similarity search - Domain/homology
Biological speciesCicer arietinum (chickpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKumar, S. / Singh, A. / Yamini, S. / Bhushan, A. / Dey, S. / Sharma, S. / Singh, T.P.
CitationJournal: Protein J. / Year: 2015
Title: Crystal Structure of Mg(2+) Containing Hemopexin-Fold Protein from Kabuli Chana (Chickpea-White, CW-25) at 2.45 angstrom Resolution Reveals Its Metal Ion Transport Property
Authors: Kumar, S. / Singh, A. / Yamini, S. / Dey, S. / Singh, T.P.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...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_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8444
Polymers50,7952
Non-polymers492
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-23 kcal/mol
Surface area18620 Å2
Unit cell
Length a, b, c (Å)80.481, 80.481, 69.177
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Lectin


Mass: 25397.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cicer arietinum (chickpea) / References: UniProt: G1K3R9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Magnesium acetate tetra hydrate, 0.1M sodiun cacodylate trihydrate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 22, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.516
11K, H, -L20.484
ReflectionResolution: 2.45→69.7 Å / Num. all: 17005 / Num. obs: 17005 / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.3
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.4 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data collection
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HSD

4hsd


Resolution: 2.45→69.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.194 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19388 890 5 %RANDOM
Rwork0.15066 ---
obs0.15284 17005 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.079 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å20 Å20 Å2
2--3.36 Å20 Å2
3----6.72 Å2
Refinement stepCycle: LAST / Resolution: 2.45→69.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 2 222 3816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023688
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9534978
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1325446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.223.444180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98115602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5321520
X-RAY DIFFRACTIONr_chiral_restr0.1340.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212874
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_it1.6922.0841790
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.583.1182234
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8292.0951898
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.83117.155787
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: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 49 -
Rwork0.179 1147 -
obs--86.17 %

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