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- PDB-1jpb: Sperm Whale met-Myoglobin (low temperature; high pressure) -

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Basic information

Entry
Database: PDB / ID: 1jpb
TitleSperm Whale met-Myoglobin (low temperature; high 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 / SYNCHROTRON / Resolution: 1.7 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)18,2366
Polymers17,2351
Non-polymers1,0015
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.800, 30.700, 34.390
Angle α, β, γ (deg.)90.00, 105.61, 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.: 4 / 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.: 146 / 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: 1.88 Å3/Da / Density % sol: 34.63 %
Description: 95K; 200MPa; pH6; slow cooled (1.7 K/s) to 77K while under 200MPa
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: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9503 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9503 Å / Relative weight: 1
ReflectionResolution: 1.7→26.5 Å / Num. all: 14459 / Num. obs: 14459 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 3.8
Reflection shellResolution: 1.68→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 8.8 / Num. unique all: 2713 / % possible all: 99
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

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

1vxh


Resolution: 1.7→26.33 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 578524.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: residues 152 and 153 were disordered
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1395 9.9 %RANDOM
Rwork0.209 ---
obs-14136 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.1254 Å2 / ksol: 0.428176 e/Å3
Displacement parametersBiso mean: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å21.13 Å2
2--0.32 Å20 Å2
3---1.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-26.54 Å
Luzzati sigma a0.13 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.7→26.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 63 146 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 241 10.2 %
Rwork0.221 2118 -
obs--98.9 %
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: 26.5 Å / Num. reflection obs: 14137 / σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.969
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.291 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.221

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