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- PDB-109m: SPERM WHALE MYOGLOBIN D122N ETHYL ISOCYANIDE AT PH 9.0 -

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Basic information

Entry
Database: PDB / ID: 109m
TitleSPERM WHALE MYOGLOBIN D122N ETHYL ISOCYANIDE AT PH 9.0
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / LIGAND BINDING / OXYGEN STORAGE / OXYGEN BINDING / HEME
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHYL ISOCYANIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsSmith, R.D. / Olson, J.S. / Phillips Jr., G.N.
CitationJournal: Thesis, Rice / Year: 1999
Title: Correlations between Bound N-Alkyl Isocyanide Orientations and Pathways for Ligand Binding in Recombinant Myoglobins
Authors: Smith, R.D.
History
DepositionDec 22, 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 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Mar 10, 2021Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / struct_conn ...pdbx_distant_solvent_atoms / struct_conn / struct_conn_type / struct_site
Item: _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)18,1344
Polymers17,3651
Non-polymers7693
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)91.486, 91.486, 45.874
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: 17365.164 Da / Num. of mol.: 1 / Mutation: INS(M0), D122N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Tissue: SKELETAL MUSCLE / Cellular location: CYTOPLASM / Organ: SKELETALSkeleton / Plasmid: PEMBL 19+ / Production host: Escherichia coli (E. coli) / Strain (production host): PHAGE RESISTANT TB1 / 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: Chemical ChemComp-ENC / ETHYL ISOCYANIDE / Isocyanide


Mass: 56.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growpH: 9
Details: 3.0 M AMMONIUM SULFATE, 20 MM TRIS, 1MM EDTA, PH 9.0

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1993 / Details: PINHOLE COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→6 Å / Num. obs: 15743 / % possible obs: 80.7 % / Observed criterion σ(I): 0 / Redundancy: 4.35 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.044
Reflection shellResolution: 1.83→1.84 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.268 / % possible all: 85.6

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SPERM WHALE MYOGLOBIN 0M, D122N (DEOXY)

Resolution: 1.83→5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1411 9.9 %RANDOM
Rwork0.148 ---
obs0.148 14265 77.1 %-
Displacement parametersBiso mean: 20.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.83→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 47 202 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.111.5
X-RAY DIFFRACTIONx_mcangle_it2.512
X-RAY DIFFRACTIONx_scbond_it7.062.5
X-RAY DIFFRACTIONx_scangle_it9.62.5
LS refinement shellResolution: 1.83→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.242 166 9.9 %
Rwork0.215 1504 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.HEMETOPOLOGY.HEME
X-RAY DIFFRACTION3PARAMETER.ETNCTOPOLOGY.ETNC
X-RAY DIFFRACTION4PARAM19.SOLVTOPH19.SOLV

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