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- PDB-3a9m: Crystal structure of a hemoglobin component V from Propsilocerus ... -

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Basic information

Entry
Database: PDB / ID: 3a9m
TitleCrystal structure of a hemoglobin component V from Propsilocerus akamusi (pH9.0 coordinates)
ComponentsHemoglobin V
KeywordsOXYGEN TRANSPORT / hemoglobin / insect / Diptera / Propsilocerus akamusi / midge larva / Heme / Transport
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin V
Similarity search - Component
Biological speciesTokunagayusurika akamusi (insect)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKuwada, T. / Hasegawa, T. / Takagi, T. / Shishikura, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: pH-dependent structural changes in haemoglobin component V from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera)
Authors: Kuwada, T. / Hasegawa, T. / Takagi, T. / Sato, I. / Shishikura, F.
History
DepositionOct 30, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8643
Polymers17,2191
Non-polymers6442
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.580, 64.510, 72.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hemoglobin V


Mass: 17219.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tokunagayusurika akamusi (insect) / Tissue: larval hemolymph / References: UniProt: Q7M422
#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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG3350, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 7, 2009
RadiationMonochromator: confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→24.68 Å / Num. obs: 15253 / % possible obs: 100 % / Redundancy: 13.72 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 13.51 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 15.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNX2005refinement
CrystalCleardata reduction
CrystalCleardata scaling
CNX2005phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X3K

1x3k


Resolution: 1.8→24.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 911398.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1544 10.1 %RANDOM
Rwork0.204 ---
obs0.206 15229 99.7 %-
all-15252 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 95.3113 Å2 / ksol: 0.472405 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---2.16 Å20 Å2
3---2.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 45 316 1574
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.431.5
X-RAY DIFFRACTIONc_mcangle_it42
X-RAY DIFFRACTIONc_scbond_it4.642
X-RAY DIFFRACTIONc_scangle_it5.872.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 236 9.5 %
Rwork0.221 2257 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.parmprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3PaV-heme.paramPaV-heme.top
X-RAY DIFFRACTION4cmo_xplor.paramcmo_xplor.top

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