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- PDB-1jp6: Sperm Whale met-Myoglobin (room temperature; room pressure) -

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Basic information

Entry
Database: PDB / ID: 1jp6
TitleSperm Whale met-Myoglobin (room temperature; room pressure)
Componentsmyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN STORAGE-TRANSPORT complex
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsUrayama, P. / Gruner, S.M. / Phillips Jr., G.N.
CitationJournal: Structure / Year: 2002
Title: Probing substates in sperm whale myoglobin using high-pressure crystallography.
Authors: Urayama, P. / Phillips Jr., G.N. / Gruner, S.M.
History
DepositionAug 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / 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: myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0444
Polymers17,2351
Non-polymers8093
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.450, 30.930, 34.730
Angle α, β, γ (deg.)90.00, 105.73, 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) / 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.93 Å3/Da / Density % sol: 36.36 % / Description: 295K; 0.1MPa; pH6
Crystal growTemperature: 298 K / Method: batch / pH: 6 / Details: ammonium sulfate, pH 6, batch, temperature 298K
Crystal grow
*PLUS
Method: batch method / PH range low: 6 / PH range high: 5.5
Components of the solutions
*PLUS
Conc.: 72-78 %sat / Common name: ammonium sulfate / Details: pH5.5-6.0

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Sep 8, 1997
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.3→9.2 Å / Num. all: 5870 / Num. obs: 5870 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.056 / Mean I/σ(I) obs: 15.6 / Num. unique all: 825 / % possible all: 94.5
Reflection shell
*PLUS
% possible obs: 94.5 %

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Processing

Software
NameVersionClassification
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementStarting model: PDB ENTRY 1VXH

1vxh


Resolution: 2.3→9.18 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 762440.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: residue 153 was disordered
RfactorNum. reflection% reflectionSelection details
Rfree0.218 633 10.9 %RANDOM
Rwork0.162 ---
obs-5811 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.7685 Å2 / ksol: 0.397049 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-0.78 Å2
2--1.97 Å20 Å2
3----1.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.21 Å
Luzzati d res low-9.2 Å
Luzzati sigma a0.21 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→9.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 53 54 1319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.224 93 10.5 %
Rwork0.166 791 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3HEME.PARAMHEME.TOP
X-RAY DIFFRACTION4SO4.PARAMSO4.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 9.2 Å / Num. reflection obs: 5853 / σ(F): 2 / % reflection Rfree: 10.9 % / Rfactor obs: 0.16 / Rfactor Rfree: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.021
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.224 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.166

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