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- PDB-1f5o: 2.9 ANGSTROM CRYSTAL STRUCTURE OF DEOXYGENATED LAMPREY HEMOGLOBIN... -

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Basic information

Entry
Database: PDB / ID: 1f5o
Title2.9 ANGSTROM CRYSTAL STRUCTURE OF DEOXYGENATED LAMPREY HEMOGLOBIN V IN THE SPACE GROUP P2(1)2(1)2(1)
ComponentsHEMOGLOBIN V
KeywordsOXYGEN STORAGE/TRANSPORT / Hemoglobin / Heme / Lamprey / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / oxidoreductase activity / iron ion binding / heme binding
Similarity search - Function
Globin, lamprey/hagfish 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 / Globin-5
Similarity search - Component
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsHeaslet, H.A. / Royer Jr., W.E.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Crystalline ligand transitions in lamprey hemoglobin. Structural evidence for the regulation of oxygen affinity.
Authors: Heaslet, H.A. / Royer Jr., W.E.
#1: Journal: Structure / Year: 1999
Title: The 2.7 Angstrom Crystal Structure of Deoxygentated Hemoglobin from the Sea Lamprey (Petromyzon Marinus): Structural Basis for a Lowered Oxygen Affinity and Bohr Effect.
Authors: Heaslet, H.A. / Royer Jr., W.E.
History
DepositionJun 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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

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Assembly

Deposited unit
A: HEMOGLOBIN V
B: HEMOGLOBIN V
C: HEMOGLOBIN V
D: HEMOGLOBIN V
E: HEMOGLOBIN V
F: HEMOGLOBIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,43712
Polymers97,7386
Non-polymers3,6996
Water21612
1
A: HEMOGLOBIN V
B: HEMOGLOBIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8124
Polymers32,5792
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HEMOGLOBIN V
D: HEMOGLOBIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8124
Polymers32,5792
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: HEMOGLOBIN V
F: HEMOGLOBIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8124
Polymers32,5792
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.5, 96.2, 146.1
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
DetailsThe physiologically relevant assembly is a homodimer in which the subunits are related by a twofold axis of symmetry. / A hexameric assembly is observed upon application of crystallographic symmetry operators. The subunits in the hexamer are arranged as one turn of an approximately three-fold screw.

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Components

#1: Protein
HEMOGLOBIN V


Mass: 16289.707 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Petromyzon marinus (sea lamprey) / References: UniProt: P02208
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 296 K / Method: small tubes / pH: 6.8
Details: 25% PEG 4K, 170mM phosphate buffer, pH 6.8, SMALL TUBES, temperature 296K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %PEG400011
2170 mMphosphate11

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 138470 / Num. obs: 25042 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.369 / Num. unique all: 2472 / % possible all: 95.1
Reflection
*PLUS
Num. measured all: 138470
Reflection shell
*PLUS
% possible obs: 95.4 % / Mean I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.9→8 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: Simulated annealing, Powell minimization and group B-factor refinements using tight non-crystallographic symmetry restraints (wa=300). ALTERNATE CRYSTAL FORM FOR DEOXY LHBV WITH SIX MONOMERS ...Details: Simulated annealing, Powell minimization and group B-factor refinements using tight non-crystallographic symmetry restraints (wa=300). ALTERNATE CRYSTAL FORM FOR DEOXY LHBV WITH SIX MONOMERS IN THE ASYMMETRIC UNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2223 -RANDOM
Rwork0.192 ---
all-138470 --
obs-25042 95.5 %-
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6864 0 258 12 7134
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.383
X-RAY DIFFRACTIONc_improper_angle_d0.848
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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