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- PDB-6hit: The crystal structure of haemoglobin from Atlantic cod -

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Basic information

Entry
Database: PDB / ID: 6hit
TitleThe crystal structure of haemoglobin from Atlantic cod
Components
  • Hemoglobin alpha 2 chain
  • Hemoglobin beta 4 chain
KeywordsOXYGEN TRANSPORT / Haemoglobin Atlantic cod Gadus morhua
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 / Hemoglobin beta 4 / Hemoglobin alpha 2 / Hemoglobin subunit alpha-2
Similarity search - Component
Biological speciesGadus morhua (Atlantic cod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHelland, R. / Bjorkeng, E.K. / Rothweiler, U. / Sydnes, M.O. / Pampanin, D.M.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway229153 Norway
Research Council of Norway247732 Norway
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: The crystal structure of haemoglobin from Atlantic cod.
Authors: Helland, R. / Bjorkeng, E.K. / Rothweiler, U. / Sydnes, M.O. / Pampanin, D.M.
History
DepositionAug 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 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_unobs_or_zero_occ_residues / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin alpha 2 chain
B: Hemoglobin beta 4 chain
C: Hemoglobin alpha 2 chain
D: Hemoglobin beta 4 chain
E: Hemoglobin alpha 2 chain
F: Hemoglobin beta 4 chain
G: Hemoglobin alpha 2 chain
H: Hemoglobin beta 4 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,16016
Polymers128,2288
Non-polymers4,9328
Water0
1
A: Hemoglobin alpha 2 chain
B: Hemoglobin beta 4 chain
C: Hemoglobin alpha 2 chain
D: Hemoglobin beta 4 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5808
Polymers64,1144
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-111 kcal/mol
Surface area22360 Å2
MethodPISA
2
E: Hemoglobin alpha 2 chain
F: Hemoglobin beta 4 chain
G: Hemoglobin alpha 2 chain
H: Hemoglobin beta 4 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5808
Polymers64,1144
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-106 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.691, 103.257, 199.352
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hemoglobin alpha 2 chain / Hemoglobin alpha chain


Mass: 15713.340 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gadus morhua (Atlantic cod) / Plasmid details: blood cells / References: UniProt: B3F9D9, UniProt: O42425*PLUS
#2: Protein
Hemoglobin beta 4 chain / Hemoglobin beta chain


Mass: 16343.712 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gadus morhua (Atlantic cod) / Plasmid details: blood cells / References: UniProt: B3F9D7
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 2.51 Å3/Da / Density % sol: 51.08 % / Description: Thin needles or plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Bicine, pH 8.5, 12% PEGMME 5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 45021 / % possible obs: 98.8 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.046 / Rrim(I) all: 0.1 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.594.40.80943020.5970.4190.91797.3
9.68-47.23.80.0358130.9970.0190.0491.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.47 Å47.2 Å
Translation6.47 Å47.2 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.5.26data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 14.23 / SU ML: 0.312 / SU R Cruickshank DPI: 0.6448 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.645 / ESU R Free: 0.35
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3013 2191 4.9 %RANDOM
Rwork0.2323 ---
obs0.2356 42768 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 155.28 Å2 / Biso mean: 55.621 Å2 / Biso min: 21.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2---1.09 Å20 Å2
3---2.58 Å2
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8468 0 344 0 8812
Biso mean--57.9 --
Num. residues----1147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199064
X-RAY DIFFRACTIONr_bond_other_d0.0020.028031
X-RAY DIFFRACTIONr_angle_refined_deg1.6072.00312471
X-RAY DIFFRACTIONr_angle_other_deg1.073318369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28451143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91823.209321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.139151263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7751539
X-RAY DIFFRACTIONr_chiral_restr0.1080.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210361
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021998
LS refinement shellResolution: 2.499→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 142 -
Rwork0.327 3047 -
all-3189 -
obs--96.32 %

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