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- PDB-4bja: Globin-like protein Glb-12 from C.elegans -

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Basic information

Entry
Database: PDB / ID: 4bja
TitleGlobin-like protein Glb-12 from C.elegans
ComponentsPROTEIN GLB-12
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / GLOBIN domain-containing protein
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsDe Henau, S. / Tilleman, L. / Germani, F. / Pauwels, M. / Vlaeminck, C. / Vanfleteren, J.R. / Bert, W. / Pesce, A. / Nardini, M. / Bolognesi, M. ...De Henau, S. / Tilleman, L. / Germani, F. / Pauwels, M. / Vlaeminck, C. / Vanfleteren, J.R. / Bert, W. / Pesce, A. / Nardini, M. / Bolognesi, M. / De Wael, K. / Moens, L. / Dewilde, S. / Braeckman, B.P.
CitationJournal: Nat.Commun. / Year: 2015
Title: A Redox Signalling Globin is Essential for Reproduction in Caenorhabditis Elegans.
Authors: De Henau, S. / Tilleman, L. / Vangheel, M. / Luyckx, E. / Trashin, S. / Pauwels, M. / Germani, F. / Vlaeminck, C. / Vanfleteren, J.R. / Bert, W. / Pesce, A. / Nardini, M. / Bolognesi, M. / ...Authors: De Henau, S. / Tilleman, L. / Vangheel, M. / Luyckx, E. / Trashin, S. / Pauwels, M. / Germani, F. / Vlaeminck, C. / Vanfleteren, J.R. / Bert, W. / Pesce, A. / Nardini, M. / Bolognesi, M. / De Wael, K. / Moens, L. / Dewilde, S. / Braeckman, B.P.
History
DepositionApr 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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: PROTEIN GLB-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6167
Polymers30,6671
Non-polymers9496
Water1,982110
1
A: PROTEIN GLB-12
hetero molecules

A: PROTEIN GLB-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,23114
Polymers61,3342
Non-polymers1,89712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5780 Å2
ΔGint-91.6 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.440, 50.440, 245.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PROTEIN GLB-12 / HEMOGLOBIN


Mass: 30666.965 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q09514
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCYS6 HAS BEEN MUTATED TO SER 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: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 4.6
Details: 2 M AMMONIUM SULFATE, 0.2 M NA-ACETATE, 0.1 M NA-ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 30, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→29.85 Å / Num. obs: 23429 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.9
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.65→43.68 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.081 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY WAS DETECTED FOR RESIDUES 1-18, 167-181, AND 216-266.
RfactorNum. reflection% reflectionSelection details
Rfree0.23414 1197 5.1 %RANDOM
Rwork0.17827 ---
obs0.1811 22130 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 64 110 1677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221639
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6412.0482229
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49124.51282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38215304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.491512
X-RAY DIFFRACTIONr_chiral_restr0.1460.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211248
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_it1.641.5937
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.67621516
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6763702
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5014.5706
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.22731639
X-RAY DIFFRACTIONr_sphericity_free7.9753124
X-RAY DIFFRACTIONr_sphericity_bonded7.21831601
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 104 -
Rwork0.208 1585 -
obs--99.88 %

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