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- PDB-3wtg: Crystal structure of Emu (dromaius novaehollandiae) hemoglobin at... -

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Basic information

Entry
Database: PDB / ID: 3wtg
TitleCrystal structure of Emu (dromaius novaehollandiae) hemoglobin at 2.3 angstrom resolution
Components
  • Hemoglobin
  • Hemoglobin subunit alpha-A
KeywordsOXYGEN TRANSPORT / HEMOGLOBIN / OXYGEN AFFINITY / AVIAN / OXYGEN
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / 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 / Hemoglobin / Hemoglobin subunit alpha-A
Similarity search - Component
Biological speciesDromaius novaehollandiae (emu)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAbubakkar, M.M. / Maheshwaran, V. / Ponnuswamy, M.N. / Saraboji, K.
CitationJournal: To be Published
Title: Purification and preliminary structural studies of hemoglobin from high oxygen affinity species Emu (Dromaius novaehollandiae) at neutral pH
Authors: Abubakkar, M.M. / Saraboji, K. / Ponnuswamy, M.N.
History
DepositionApr 11, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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.ptnr3_label_seq_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_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: Hemoglobin subunit alpha-A
B: Hemoglobin
C: Hemoglobin subunit alpha-A
D: Hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,40212
Polymers63,8084
Non-polymers2,5948
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.271, 80.010, 103.559
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 subunit alpha-A


Mass: 15581.942 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dromaius novaehollandiae (emu) / References: UniProt: C6L8R0
#2: Protein Hemoglobin


Mass: 16321.864 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dromaius novaehollandiae (emu) / References: UniProt: A0A075B5G0*PLUS
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


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


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THE CHAINS B AND D DOES NOT CURRENTLY EXIST.

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 8, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 25129 / % possible obs: 99 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 6.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 6.4 / Rsym value: 0.061 / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FS4

3fs4


Resolution: 2.3→29.36 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9 / SU B: 15.922 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1259 5 %RANDOM
Rwork0.192 ---
obs0.196 23787 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 180 360 4959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224727
X-RAY DIFFRACTIONr_bond_other_d0.0010.023038
X-RAY DIFFRACTIONr_angle_refined_deg1.5792.0536472
X-RAY DIFFRACTIONr_angle_other_deg0.99137430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7265564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8124.105190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60315752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4381516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02902
X-RAY DIFFRACTIONr_mcbond_it0.7891.52833
X-RAY DIFFRACTIONr_mcbond_other0.1881.51136
X-RAY DIFFRACTIONr_mcangle_it1.48324552
X-RAY DIFFRACTIONr_scbond_it2.34731894
X-RAY DIFFRACTIONr_scangle_it3.5154.51920
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 92 -
Rwork0.218 1717 -
obs--99.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.28870.3389-0.10342.01880.18961.8311-0.07230.10130.0574-0.23570.09560.0461-0.12820.0408-0.02330.0814-0.0171-0.02950.02250.01520.024-3.68166.452.4989
22.55240.0138-0.1021.1985-0.14731.5338-0.0498-0.41320.00570.071-0.0423-0.00060.00170.01340.09210.02440.0007-0.00040.101-0.02430.0227-7.25667.015426.5259
31.83930.60710.52872.00960.67021.80460.0659-0.11120.2552-0.0398-0.08410.0991-0.0715-0.08230.01830.0180.0066-0.00550.0143-0.02760.0705-35.0472-0.4110.3389
41.6712-0.2111-0.48350.8571-0.16291.3141-0.0679-0.23-0.21180.0106-0.0189-0.01760.0560.02010.08680.03630.00860.00120.03770.03110.0334-20.0377-19.135614.2114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 138
2X-RAY DIFFRACTION1A201 - 202
3X-RAY DIFFRACTION2B1 - 146
4X-RAY DIFFRACTION2B201 - 202
5X-RAY DIFFRACTION3C1 - 138
6X-RAY DIFFRACTION3C201 - 202
7X-RAY DIFFRACTION4D1 - 146
8X-RAY DIFFRACTION4D201 - 202

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