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Basic information

Entry
Database: PDB / ID: 2zs1
TitleStructural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin
Components(Extracellular giant hemoglobin major globin subunit ...) x 4
KeywordsOxygen Storage / Oxygen transport / hemoglobin / annelida / magnesium / cooperativity / Heme / Iron / Metal-binding / Secreted / Transport
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily ...Globin, extracellular / Erythrocruorin / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Extracellular giant hemoglobin major globin subunit B1 / Extracellular giant hemoglobin major globin subunit A2 / Extracellular giant hemoglobin major globin subunit B2 / Extracellular giant hemoglobin major globin subunit A1
Similarity search - Component
Biological speciesOligobrachia mashikoi (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNumoto, N. / Nakagawa, T. / Kita, A. / Sasayama, Y. / Fukumori, Y. / Miki, K.
CitationJournal: Biochemistry / Year: 2008
Title: Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin
Authors: Numoto, N. / Nakagawa, T. / Kita, A. / Sasayama, Y. / Fukumori, Y. / Miki, K.
History
DepositionSep 2, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_conn_angle / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular giant hemoglobin major globin subunit A1
B: Extracellular giant hemoglobin major globin subunit A2
C: Extracellular giant hemoglobin major globin subunit B2
D: Extracellular giant hemoglobin major globin subunit B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,03720
Polymers60,8314
Non-polymers3,20616
Water11,584643
1
A: Extracellular giant hemoglobin major globin subunit A1
B: Extracellular giant hemoglobin major globin subunit A2
C: Extracellular giant hemoglobin major globin subunit B2
D: Extracellular giant hemoglobin major globin subunit B1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)384,221120
Polymers364,98424
Non-polymers19,23896
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
2
A: Extracellular giant hemoglobin major globin subunit A1
B: Extracellular giant hemoglobin major globin subunit A2
C: Extracellular giant hemoglobin major globin subunit B2
D: Extracellular giant hemoglobin major globin subunit B1
hetero molecules

A: Extracellular giant hemoglobin major globin subunit A1
B: Extracellular giant hemoglobin major globin subunit A2
C: Extracellular giant hemoglobin major globin subunit B2
D: Extracellular giant hemoglobin major globin subunit B1
hetero molecules

A: Extracellular giant hemoglobin major globin subunit A1
B: Extracellular giant hemoglobin major globin subunit A2
C: Extracellular giant hemoglobin major globin subunit B2
D: Extracellular giant hemoglobin major globin subunit B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,11160
Polymers182,49212
Non-polymers9,61948
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area46390 Å2
ΔGint-439 kcal/mol
Surface area60350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.302, 111.302, 274.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-7152-

HOH

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Components

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Extracellular giant hemoglobin major globin subunit ... , 4 types, 4 molecules ABCD

#1: Protein Extracellular giant hemoglobin major globin subunit A1 / Major globin chain b


Mass: 15188.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q7M419
#2: Protein Extracellular giant hemoglobin major globin subunit A2 / Major globin chain a5


Mass: 15327.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q7M413
#3: Protein Extracellular giant hemoglobin major globin subunit B2 / Major globin chain c


Mass: 15621.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q7M418
#4: Protein Extracellular giant hemoglobin major globin subunit B1 / Major globin chain d


Mass: 14693.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q5KSB7

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Non-polymers , 6 types, 659 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.34 % / Mosaicity: 0.524 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 10000, 0.2M Tris-HCl pH 8.0, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2007
Details: Rotated-inclined double-crystal monochromator, rhodium-coated horizontal mirror
RadiationMonochromator: rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 72136 / Num. obs: 72136 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.053 / Χ2: 1.062 / Net I/σ(I): 29.622
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 7126 / Rsym value: 0.453 / Χ2: 1.221 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.006data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D2M

2d2m


Resolution: 1.7→47.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3861989.57 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3623 5 %RANDOM
Rwork0.18 ---
obs0.18 72075 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.2915 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---1.03 Å20 Å2
3---2.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 0 218 643 5200
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.254 340 4.8 %
Rwork0.222 6777 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion_mg.parion_mg.top
X-RAY DIFFRACTION4hem_o2_100_185_mo.paramhem_o2_final_mo.top
X-RAY DIFFRACTION5gol_final.paramgol_final.top

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