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- PDB-1x9f: Hemoglobin Dodecamer from Lumbricus Erythrocruorin -

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Basic information

Entry
Database: PDB / ID: 1x9f
TitleHemoglobin Dodecamer from Lumbricus Erythrocruorin
Components
  • Globin II, extracellular
  • Globin III, extracellular
  • Globin IV, extracellular
  • hemoglobin chain d1
KeywordsOXYGEN STORAGE/TRANSPORT / Crystal / Dodecamer / Allosteric / OXYGEN STORAGE-TRANSPORT COMPLEX
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 / Erythrocruorin / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Globin, extracellular / Erythrocruorin / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Extracellular globin / Extracellular globin-2 / Extracellular globin-3 / Extracellular globin-4
Similarity search - Component
Biological speciesLumbricus terrestris (common earthworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsStrand, K. / Knapp, J.E. / Bhyravbhatla, B. / Royer Jr., W.E.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the hemoglobin dodecamer from lumbricus erythrocruorin: allosteric core of giant annelid respiratory complexes
Authors: Strand, K. / Knapp, J.E. / Bhyravbhatla, B. / Royer Jr., W.E.
History
DepositionAug 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Apr 3, 2024Group: Advisory / Data collection ...Advisory / 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_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _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 / _struct_ref_seq_dif.details / _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 IV, extracellular
B: Globin II, extracellular
C: Globin III, extracellular
D: hemoglobin chain d1
E: Globin IV, extracellular
F: Globin II, extracellular
G: Globin III, extracellular
H: hemoglobin chain d1
I: Globin IV, extracellular
J: Globin II, extracellular
K: Globin III, extracellular
L: hemoglobin chain d1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,48539
Polymers201,46612
Non-polymers8,01927
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45090 Å2
ΔGint-404 kcal/mol
Surface area66890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.225, 172.071, 202.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

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Protein , 4 types, 12 molecules AEIBFJCGKDHL

#1: Protein Globin IV, extracellular / / Erythrocruorin / Globin A


Mass: 17566.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / Organ: blood / References: UniProt: P13579
#2: Protein Globin II, extracellular / / Erythrocruorin / Globin AIII / Globin B


Mass: 16268.229 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / Organ: blood / References: UniProt: P02218
#3: Protein Globin III, extracellular / / Erythrocruorin / Globin C


Mass: 17331.793 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / Organ: blood / References: UniProt: P11069
#4: Protein hemoglobin chain d1


Mass: 15988.263 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lumbricus terrestris (common earthworm) / Organ: blood / References: UniProt: O61233

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Non-polymers , 4 types, 291 molecules

#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 2.8M Na phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 281.0K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU200H11.5418
SYNCHROTRONAPS 14-BM-C21
Detector
TypeIDDetector
RIGAKU RAXIS IIC1IMAGE PLATE
ADSC QUANTUM 42CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Yale MirrorsSINGLE WAVELENGTHMx-ray1
2Beamline opticsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionResolution: 2.6→105.41 Å / Num. all: 74920 / Num. obs: 74920 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3.8 Structure of the whole molecule

Resolution: 2.6→105.41 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.888 / SU B: 9.526 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.524 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24615 3337 5 %RANDOM
Rwork0.21316 ---
all0.21481 74920 --
obs0.21481 63085 88.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.318 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2---0.87 Å20 Å2
3---2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.6→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14028 0 555 264 14847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02114987
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.98320434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.23651731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02723.417720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11152481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.06615111
X-RAY DIFFRACTIONr_chiral_restr0.0830.22121
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211538
X-RAY DIFFRACTIONr_nbd_refined0.2970.28104
X-RAY DIFFRACTIONr_nbtor_refined0.3040.210257
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2529
X-RAY DIFFRACTIONr_metal_ion_refined0.2010.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.211
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 255 -
Rwork0.306 4470 -
obs-4470 86.63 %

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