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- PDB-5eui: Structure of predicted ancestral pika hemoglobin -

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Basic information

Entry
Database: PDB / ID: 5eui
TitleStructure of predicted ancestral pika hemoglobin
Components
  • HBA protein
  • HBB protein
KeywordsOXYGEN TRANSPORT / Hemoglobin / Pika / oxygen-transport / recombinant
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 / HBB protein / HBA protein
Similarity search - Component
Biological speciesOchotona princeps (American pika)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsInoguchi, N. / Chandrasekhar, N. / Storz, J.F. / Moriyama, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL087216-07 United States
National Science Foundation (NSF, United States)MCB-151763 6 United States
CitationJournal: To Be Published
Title: structure of predicted pika ancestral hemoglobin at 1.45 Angstroms resolution.
Authors: Inoguchi, N. / Natarajan, C. / Storz, J.F. / Moriyama, H.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HBA protein
B: HBB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3234
Polymers31,0902
Non-polymers1,2332
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-48 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.350, 91.412, 103.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HBA protein


Mass: 15216.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochotona princeps (American pika) / Gene: HBA / Production host: Escherichia coli (E. coli) / References: UniProt: U5KQB1
#2: Protein HBB protein


Mass: 15874.138 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochotona princeps (American pika) / Gene: HBB / Production host: Escherichia coli (E. coli) / References: UniProt: U5KNG4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThis hemoglobin is the reconstructed ancestor of O. princeps and O. collaris

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 299 K / Method: microbatch / pH: 8
Details: PEG 3350, sodium phosphate, potassium phosphate, calcium chloride

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.45→30.29 Å / Num. obs: 52380 / % possible obs: 97.94 % / Redundancy: 7 % / Rmerge(I) obs: 0.0594 / Net I/σ(I): 26.96

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DN1

2dn1


Resolution: 1.45→30.289 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 1993 3.82 %ramdon selection
Rwork0.1943 ---
obs0.195 52222 97.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→30.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 86 482 2706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072311
X-RAY DIFFRACTIONf_angle_d1.1423164
X-RAY DIFFRACTIONf_dihedral_angle_d12.981781
X-RAY DIFFRACTIONf_chiral_restr0.041339
X-RAY DIFFRACTIONf_plane_restr0.006395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4503-1.48650.26841440.22833605X-RAY DIFFRACTION100
1.4865-1.52670.26311440.21293652X-RAY DIFFRACTION100
1.5267-1.57170.22931430.19633614X-RAY DIFFRACTION100
1.5717-1.62240.21251460.19253654X-RAY DIFFRACTION100
1.6224-1.68040.24341450.19933654X-RAY DIFFRACTION100
1.6804-1.74760.18961430.19463613X-RAY DIFFRACTION100
1.7476-1.82720.24771440.20173646X-RAY DIFFRACTION100
1.8272-1.92350.21531440.22823612X-RAY DIFFRACTION98
1.9235-2.0440.21521430.20323621X-RAY DIFFRACTION99
2.044-2.20170.20951450.18593658X-RAY DIFFRACTION100
2.2017-2.42320.23021410.19113566X-RAY DIFFRACTION97
2.4232-2.77370.18331470.18713700X-RAY DIFFRACTION100
2.7737-3.49370.2011480.18453707X-RAY DIFFRACTION100
3.4937-30.29590.20661160.19222927X-RAY DIFFRACTION76

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