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- PDB-4wch: Structure of Isolated D Chain of Gigant Hemoglobin from Glossosco... -

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Entry
Database: PDB / ID: 4wch
TitleStructure of Isolated D Chain of Gigant Hemoglobin from Glossoscolex paulistus
ComponentsIsolated Chain D of Gigant Hemoglobin from Glossoscolex Paulistus
KeywordsOXYGEN STORAGE / Globin / D chain.
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / extracellular region
Similarity search - Function
Globin, extracellular / 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 / Extracellular globin
Similarity search - Component
Biological speciesGlossoscolex paulistus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsBachega, J.F.R. / Maluf, F.V. / Pereira, H.M. / Brandao-Neto, J. / Tabak, M. / Garratt, R.C. / Horjales, E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The structure of the giant haemoglobin from Glossoscolex paulistus.
Authors: Ruggiero Bachega, J.F. / Vasconcelos Maluf, F. / Andi, B. / D'Muniz Pereira, H. / Falsarella Carazzollea, M. / Orville, A.M. / Tabak, M. / Brandao-Neto, J. / Garratt, R.C. / Horjales Reboredo, E.
History
DepositionSep 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_nat ...diffrn_source / entity_src_nat / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_nat.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
D: Isolated Chain D of Gigant Hemoglobin from Glossoscolex Paulistus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7163
Polymers16,0671
Non-polymers6482
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Isolated Chain D of Gigant Hemoglobin from Glossoscolex Paulistus
hetero molecules

D: Isolated Chain D of Gigant Hemoglobin from Glossoscolex Paulistus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4316
Polymers32,1342
Non-polymers1,2974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x,y,-z+21
Buried area4330 Å2
ΔGint-51 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.110, 63.150, 78.386
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11D-16-

ARG

21D-306-

HOH

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Components

#1: Protein Isolated Chain D of Gigant Hemoglobin from Glossoscolex Paulistus


Mass: 16067.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glossoscolex paulistus (invertebrata) / References: UniProt: A0A0M3KKZ2*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.05 Å3/Da / Density % sol: 39.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.5M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.05→43.97 Å / Num. obs: 8521 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 27.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.036 / Net I/σ(I): 19.5 / Num. measured all: 36867 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.05-2.114.30.9772.528366570.6460.52499.3
8.94-43.973.80.018724951290.9990.0199.2

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Processing

Software
NameVersionClassification
XDS0.3.8data reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
GDAdata collection
RefinementResolution: 2.05→43.968 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 823 9.67 %
Rwork0.2068 7688 -
obs0.2096 8511 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.95 Å2 / Biso mean: 31.2173 Å2 / Biso min: 10.33 Å2
Refinement stepCycle: final / Resolution: 2.05→43.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 75 54 1266
Biso mean--25.26 32.65 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051221
X-RAY DIFFRACTIONf_angle_d0.9671661
X-RAY DIFFRACTIONf_chiral_restr0.053167
X-RAY DIFFRACTIONf_plane_restr0.004210
X-RAY DIFFRACTIONf_dihedral_angle_d17.829423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.17850.32041330.30861259X-RAY DIFFRACTION99
2.1785-2.34670.33761250.25091262X-RAY DIFFRACTION99
2.3467-2.58280.26211420.21671278X-RAY DIFFRACTION100
2.5828-2.95640.25991480.22531260X-RAY DIFFRACTION99
2.9564-3.72450.22351510.20181265X-RAY DIFFRACTION99
3.7245-43.97830.17861240.16861364X-RAY DIFFRACTION98

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