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- PDB-1l2k: Neutron Structure Determination of Sperm Whale Met-Myoglobin at 1... -

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Basic information

Entry
Database: PDB / ID: 1l2k
TitleNeutron Structure Determination of Sperm Whale Met-Myoglobin at 1.5A Resolution.
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / NEUTRON STRUCTURE / HYDROGEN ATOMS / HYDRATION STRUCTURE / HEME PROTEIN / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DEUTERATED WATER / PROTOPORPHYRIN IX CONTAINING FE / AMMONIUM CATION WITH D / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 1.5 Å
AuthorsOstermann, A. / Tanaka, I. / Engler, N. / Niimura, N. / Parak, F.G.
Citation
Journal: Biophys.Chem. / Year: 2002
Title: Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 A resolution.
Authors: Ostermann, A. / Tanaka, I. / Engler, N. / Niimura, N. / Parak, F.G.
#1: Journal: CURR.OPIN.STRUCT.BIOL. / Year: 1999
Title: Neutrons Expand the Field of Structural Biology
Authors: Niimura, N.
History
DepositionFeb 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0665
Polymers17,2351
Non-polymers8314
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.530, 30.870, 34.870
Angle α, β, γ (deg.)90.00, 105.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYOGLOBIN


Mass: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / Tissue: muscle / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ND4 / AMMONIUM CATION WITH D


Mass: 22.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: batch crystallization / pH: 6.8
Details: AMMONIUM SULFATE, POTASSIUM PHOSPHATE, pH 6.8, BATCH CRYSTALLIZATION, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM11KH2PO4
22.9 Mammonium sulfate11pH6.8

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: NUCLEAR REACTOR / Beamline: BIX-3 (1G-A BEAM PORT) / Type: JRR-3M, GUIDE 1G-A, BIX-3 / Wavelength: 2.35 Å
DetectorType: MACSCIENCE / Detector: NEUTRON IMAGE PLATE / Date: Feb 5, 2000
RadiationMonochromator: ELASTICALLY BENT SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.35 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 19135 / % possible obs: 87.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 6.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1458 / % possible all: 67
Reflection
*PLUS
Lowest resolution: 22 Å / Num. measured all: 55899 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 67 % / Num. unique obs: 1458 / Num. measured obs: 3041 / Rmerge(I) obs: 0.249

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementStarting model: X-RAY STRUCTURE

Resolution: 1.5→22.7 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
Details: X-PLOR 3.851 was also used in refinement. THE STANDARD TOPOLOGY AND PARAMETER FILES WERE CHANGED FOR SEVERAL HYDROGEN ATOM PARAMETERS TO MEET THE REQUIREMENTS OF THE NEUTRON STRUCTURE ...Details: X-PLOR 3.851 was also used in refinement. THE STANDARD TOPOLOGY AND PARAMETER FILES WERE CHANGED FOR SEVERAL HYDROGEN ATOM PARAMETERS TO MEET THE REQUIREMENTS OF THE NEUTRON STRUCTURE REFINEMENT. THE FOLLOWING NEUTRON-SCATTERING LENGTHS WERE USED FOR THE REFINEMENT: ATOM H = -0.374 10**-12 CM. ATOM D = 0.667 10**-12 CM. ATOM C = 0.665 10**-12 CM. ATOM N = 0.921 10**-12 CM. ATOM O = 0.581 10**-12 CM. ATOM S = 0.285 10**-12 CM. ATOM FE = 0.954 10**-12 CM. DEUTERIUM ATOMS IN AMINO ACID SIDE CHAINS WERE ONLY INCLUDED INTO THE MODEL IF A SIGNIFICANT DENSITY FEATURE WAS PRESENT. OCCUPANCIES FOR THE BACKBONE AMIDE HYDROGEN ATOMS WERE REFINED (H/D EXCHANGE). FOR THE OCCUPANCY REFINEMENT NO CONSTRAINT FOR ADDING UP THE OCCUPANCIES TO 1.0 WAS USED. THE ADDED FRACTIONAL OCCUPANCY AVERAGED OVER ALL BACKBONE AMIDE GROUPS YIELDS A VALUE OF 1.09 WITH AN S.D. OF 0.125. THE VALUES GIVEN IN THIS COORDINATE FILE ARE NORMALIZED. A POSITIONAL REFINEMENT FOR THE BACKBONE AMIDE HYDROGEN ATOMS WITH WEAKENED IN-PLANE RESTRAINTS FOR THE HYDROGEN ATOM WITH RESPECT TO THE AMIDE PLANE SHOWED DEVIATIONS GREATER THAN 10 DEGREE FOR THE FOLLOWING RESIDUES: 12,15, 31,48,51,56,58,80,94,96,97,99,101,103,104,107,144. THE COORDINATES GIVEN IN THIS FILE WERE REFINED WITH NORMAL RESTRAINTS. IN HIS 97 THE HYDROGEN ATOM HE1 WHICH IS BOUND TO THE CARBON ATOM CE1 IS EXCHANGED TO DEUTERIUM. FOR SEVERAL WATER MOLECULES (DOD) ONLY THE O-ATOM AND ONE D-ATOM COULD BE OBSERVED IN THE DENSITY MAP. THE SECOND D-ATOM IS STRONGLY DISORDERED. THESE WATER MOLECULES WERE MODELED AS OD. IT DOES NOT MEAN HYDROXYL-ION. THERE IS NEARLY NO NEUTRON DENSITY FOR RESIDUE 152 AND 153. THOSE RESIDUES WERE NOT INCLUDED INTO THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1308 6.9 %RANDOM
Rwork0.2011 ---
all-19135 --
obs-19063 88.6 %-
Solvent computationSolvent model: flat model / Bsol: 120 Å2 / ksol: 0.0625 e/Å3
Displacement parametersBiso mean: 12.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.5→22.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 54 74 1331
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
NEUTRON DIFFRACTIONc_bond_d0.005
NEUTRON DIFFRACTIONc_bond_d_na
NEUTRON DIFFRACTIONc_bond_d_prot
NEUTRON DIFFRACTIONc_angle_d
NEUTRON DIFFRACTIONc_angle_d_na
NEUTRON DIFFRACTIONc_angle_d_prot
NEUTRON DIFFRACTIONc_angle_deg1
NEUTRON DIFFRACTIONc_angle_deg_na
NEUTRON DIFFRACTIONc_angle_deg_prot
NEUTRON DIFFRACTIONc_dihedral_angle_d18.3
NEUTRON DIFFRACTIONc_dihedral_angle_d_na
NEUTRON DIFFRACTIONc_dihedral_angle_d_prot
NEUTRON DIFFRACTIONc_improper_angle_d5.01
NEUTRON DIFFRACTIONc_improper_angle_d_na
NEUTRON DIFFRACTIONc_improper_angle_d_prot
NEUTRON DIFFRACTIONc_mcbond_it1.5
NEUTRON DIFFRACTIONc_mcangle_it2
NEUTRON DIFFRACTIONc_scbond_it2.2
NEUTRON DIFFRACTIONc_scangle_it2.7
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3057 111 7.2 %
Rwork0.2825 1431 -
obs-1431 72.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
NEUTRON DIFFRACTION1PROTEIN.PARAMPROTEIN-ALLHDG.TOP
NEUTRON DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
NEUTRON DIFFRACTION3PARNEUTRON.SOLTOPNEUTRON.SOL
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 22 Å / Num. reflection obs: 17824 / Num. reflection Rfree: 1311 / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg5.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.3057 / Rfactor Rwork: 0.2825

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