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- PDB-1obm: RECOMBINANT SPERM WHALE MYOGLOBIN 29F/64Q/68F/122N MUTANT (MET) -

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Basic information

Entry
Database: PDB / ID: 1obm
TitleRECOMBINANT SPERM WHALE MYOGLOBIN 29F/64Q/68F/122N MUTANT (MET)
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / OXYGEN BINDING MUSCLE PROTEIN
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / 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: 1.85 Å
AuthorsBrucker, E.A. / Lile, R.A. / Phillips Jr., G.N.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Solution and crystal structures of a sperm whale myoglobin triple mutant that mimics the sulfide-binding hemoglobin from Lucina pectinata.
Authors: Nguyen, B.D. / Zhao, X. / Vyas, K. / La Mar, G.N. / Lile, R.A. / Brucker, E.A. / Phillips Jr., G.N. / Olson, J.S. / Wittenberg, J.B.
History
DepositionDec 19, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)18,1503
Polymers17,4371
Non-polymers7132
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.390, 91.390, 45.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein MYOGLOBIN /


Mass: 17437.203 Da / Num. of mol.: 1 / Mutation: INITIATOR MET, L29F, H64Q, V68F, D122N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS STRUCTURE HAS FIVE DIFFERENCES RELATIVE TO THE NATIVE. SPERM WHALE PROTEIN: AN INITIATOR ...THIS STRUCTURE HAS FIVE DIFFERENCES RELATIVE TO THE NATIVE. SPERM WHALE PROTEIN: AN INITIATOR METHIONINE, RESIDUES 29 (LEUCINE) AND 68 (VALINE) REPLACED WITH PHENYLALANINE, RESIDUE 64 (HISTIDINE) REPLACED WITH GLUTAMINE, AND RESIDUE 122 (ASPARTIC ACID) REPLACED WITH ASPARAGINE.

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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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growpH: 9 / Details: pH 9
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.4-2.7 Mammonium salfate11
220 mMTris-HCl11
31 mMEDTA11

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 20852 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057
Reflection
*PLUS
Num. measured all: 74100
Reflection shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 5 Å / % possible obs: 87.3 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XDSdata scaling
X-PLOR3.1phasing
RefinementResolution: 1.85→5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.168 --
obs0.168 15526 87.3 %
Refinement stepCycle: LAST / Resolution: 1.85→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1231 0 49 151 1431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.554
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.07
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.608
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.85→1.93 Å
RfactorNum. reflection% reflection
Rwork0.265 1725 -
obs--78.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.HEMETOPOLOGY.HEME
X-RAY DIFFRACTION3PARAM19.SOLVTOPH19.SOLV
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.07
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.608

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