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- PDB-1f5p: 2.9 ANGSTROM CRYSTAL STRUCTURE OF LAMPREY HEMOGLOBIN THAT HAS BEE... -

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Basic information

Entry
Database: PDB / ID: 1f5p
Title2.9 ANGSTROM CRYSTAL STRUCTURE OF LAMPREY HEMOGLOBIN THAT HAS BEEN EXPOSED TO CARBON MONOXIDE.
ComponentsHEMOGLOBIN V
KeywordsOXYGEN STORAGE/TRANSPORT / crystalline ligand transitions / 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
CARBON MONOXIDE / 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 1.0Jun 28, 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.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_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

Downloads & links

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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)101,60518
Polymers97,7386
Non-polymers3,86712
Water1086
1
A: HEMOGLOBIN V
B: HEMOGLOBIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8686
Polymers32,5792
Non-polymers1,2894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HEMOGLOBIN V
D: HEMOGLOBIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8686
Polymers32,5792
Non-polymers1,2894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: HEMOGLOBIN V
F: HEMOGLOBIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8686
Polymers32,5792
Non-polymers1,2894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.5, 96.2, 145.1
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe physiologically relevent 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: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCrystalline ligand transition experiments.

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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: 2.94 Å3/Da / Density % sol: 58.23 %
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: Mar 8, 2000
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: 59776 / Num. obs: 19804 / % possible obs: 75.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.01 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.376 / Num. unique all: 2036 / % possible all: 79.1
Reflection
*PLUS
Num. obs: 24593 / % possible obs: 93.9 % / Num. measured all: 81837 / Rmerge(I) obs: 0.118
Reflection shell
*PLUS
% possible obs: 79.3 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.9→10 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: Simulated annealing, Powell minimization, group B-factor and group occupancy refinements using tight non-crystallographic symmetry restraints (wa=200) on the protein except for residue 73.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1803 -RANDOM
Rwork0.206 ---
all-59776 --
obs-19804 75.6 %-
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6884 0 270 6 7160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.586
X-RAY DIFFRACTIONc_improper_angle_d1.064
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 19647 / Num. reflection Rfree: 2168 / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.206 / Highest resolution: 2.9 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.586
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.064

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