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- PDB-2wth: Low resolution 3D structure of C.elegans globin-like protein (GLB... -

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Basic information

Entry
Database: PDB / ID: 2wth
TitleLow resolution 3D structure of C.elegans globin-like protein (GLB-1): P3121 crystal form
ComponentsGLOBIN-LIKE PROTEIN
KeywordsOXYGEN TRANSPORT / METAL-BINDING
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Globin, nematode / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Globin-like protein
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGeuens, E. / Hoogewijs, D. / Nardini, M. / Vinck, E. / Pesce, A. / Kiger, L. / Fago, A. / Tilleman, L. / De Henau, S. / Marden, M. ...Geuens, E. / Hoogewijs, D. / Nardini, M. / Vinck, E. / Pesce, A. / Kiger, L. / Fago, A. / Tilleman, L. / De Henau, S. / Marden, M. / Weber, R.E. / Van Doorslaer, S. / Vanfleteren, J. / Moens, L. / Bolognesi, M. / Dewilde, S.
CitationJournal: Bmc Biochem. / Year: 2010
Title: Globin-Like Proteins in Caenorhabditis Elegans: In Vivo Localization, Ligand Binding and Structural Properties.
Authors: Geuens, E. / Hoogewijs, D. / Nardini, M. / Vinck, E. / Pesce, A. / Kiger, L. / Fago, A. / Tilleman, L. / De Henau, S. / Marden, M. / Weber, R.E. / Van Doorslaer, S. / Vanfleteren, J. / ...Authors: Geuens, E. / Hoogewijs, D. / Nardini, M. / Vinck, E. / Pesce, A. / Kiger, L. / Fago, A. / Tilleman, L. / De Henau, S. / Marden, M. / Weber, R.E. / Van Doorslaer, S. / Vanfleteren, J. / Moens, L. / Bolognesi, M. / Dewilde, S.
History
DepositionSep 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.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_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_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_conn.ptnr2_label_seq_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: GLOBIN-LIKE PROTEIN
B: GLOBIN-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,15615
Polymers37,0182
Non-polymers2,13813
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-83.4 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.681, 77.681, 145.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GLOBIN-LIKE PROTEIN


Mass: 18508.979 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30627

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Non-polymers , 5 types, 59 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 127 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 127 TO SER
Sequence detailsWITH RESPECT TO SEQUENCE PRESENT IN THE UNIPROT DATABASE, CYS127 WAS MUTATED INTO SER RESIDUE FOR ...WITH RESPECT TO SEQUENCE PRESENT IN THE UNIPROT DATABASE, CYS127 WAS MUTATED INTO SER RESIDUE FOR CRYSTALLIZATION PURPOSE

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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: 3.6 Å3/Da / Density % sol: 65.3 % / Description: NONE
Crystal growDetails: 3.0 M AMMONIUM SULPHATE, 10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→34.3 Å / Num. obs: 12777 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WTG

2wtg


Resolution: 2.8→34.28 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.819 / SU B: 39.48 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.31948 627 4.9 %RANDOM
Rwork0.269 ---
obs0.27139 12139 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.848 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.35 Å20 Å2
2--0.69 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 141 46 2775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212666
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9962.0413617
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6495314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80824.074135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44215384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.21515
X-RAY DIFFRACTIONr_chiral_restr0.0640.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022101
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21377
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21831
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7361.51578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33922445
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.15231244
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5934.51168
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 57 -
Rwork0.334 867 -
obs--98.72 %

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