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- PDB-2d2m: Structure of an extracellular giant hemoglobin of the gutless bea... -

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Basic information

Entry
Database: PDB / ID: 2d2m
TitleStructure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi
Components(Giant hemoglobin, ...) x 4
KeywordsOXYGEN STORAGE/TRANSPORT / giant hemoglobin / sulfide binding / invertebrate / pogonophora / oligobrachia mashikoi / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region
Similarity search - Function
Globin, extracellular / Erythrocruorin / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Globin, extracellular / Erythrocruorin / 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 / 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 / MIR / Resolution: 2.85 Å
AuthorsNumoto, N. / Nakagawa, T. / Kita, A. / Sasayama, Y. / Fukumori, Y. / Miki, K.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.
Authors: Numoto, N. / Nakagawa, T. / Kita, A. / Sasayama, Y. / Fukumori, Y. / Miki, K.
#1: Journal: Biochim.Biophys.Acta / Year: 2005
Title: Crystallization and preliminary X-ray crystallographic analysis of extracellular giant hemoglobin from pogonophoran Oligobrachia mashikoi.
Authors: Numoto, N. / Nakagawa, T. / Kita, A. / Sasayama, Y. / Fukumori, Y. / Miki, K.
History
DepositionSep 12, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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: Giant hemoglobin, A1(b) globin chain
B: Giant hemoglobin, A2(a5) globin chain
C: Giant hemoglobin, B2(c) globin chain
D: Giant hemoglobin, B1(d) globin chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,51812
Polymers60,9244
Non-polymers2,5948
Water23413
1
A: Giant hemoglobin, A1(b) globin chain
B: Giant hemoglobin, A2(a5) globin chain
C: Giant hemoglobin, B2(c) globin chain
D: Giant hemoglobin, B1(d) globin chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)381,10672
Polymers365,54224
Non-polymers15,56448
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_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Unit cell
Length a, b, c (Å)111.498, 111.498, 276.835
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Giant hemoglobin, ... , 4 types, 4 molecules ABCD

#1: Protein Giant hemoglobin, A1(b) globin chain / HEMOGLOBIN CHAIN A1


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 Giant hemoglobin, A2(a5) globin chain / HEMOGLOBIN CHAIN A2


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 Giant hemoglobin, B2(c) globin chain / HEMOGLOBIN CHAIN B2


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 Giant hemoglobin, B1(d) globin chain / HEMOGLOBIN CHAIN B1


Mass: 14786.386 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 , 3 types, 21 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 10000, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2004 / Details: Rh-coated mirror
RadiationMonochromator: Double-crystal monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 15821 / Num. obs: 15821 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rsym value: 0.074 / Net I/σ(I): 28.2
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 1557 / Rsym value: 0.444 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.85→50 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 3307054.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 779 5 %RANDOM
Rwork0.236 ---
all-15821 --
obs-15426 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.7641 Å2 / ksol: 0.352193 e/Å3
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å24.79 Å20 Å2
2--2.26 Å20 Å2
3----4.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 180 13 4457
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.271.5
X-RAY DIFFRACTIONc_mcangle_it17.492
X-RAY DIFFRACTIONc_scbond_it17.982
X-RAY DIFFRACTIONc_scangle_it24.192.5
LS refinement shellResolution: 2.85→2.95 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.395 63 4.3 %
Rwork0.341 1416 -
obs-1479 94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2hem_xplor_par9.txthem_xplor_top3.txt
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4o2_xplor_par.txto2_xplor_top.txt

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