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- PDB-1cp5: RECOMBINANT SPERM WHALE MYOGLOBIN L104F MUTANT (MET) -

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Basic information

Entry
Database: PDB / ID: 1cp5
TitleRECOMBINANT SPERM WHALE MYOGLOBIN L104F MUTANT (MET)
ComponentsPROTEIN (MYOGLOBIN)
KeywordsOXYGEN TRANSPORT / HEME / MUSCLE PROTEIN
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 domain 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 / OTHER / Resolution: 2.1 Å
AuthorsLiong, E.C. / Phillips Jr., G.N.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Waterproofing the heme pocket. Role of proximal amino acid side chains in preventing hemin loss from myoglobin.
Authors: Liong, E.C. / Dou, Y. / Scott, E.E. / Olson, J.S. / Phillips Jr., G.N.
History
DepositionJun 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1123
Polymers17,3991
Non-polymers7132
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.600, 91.600, 45.904
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 PROTEIN (MYOGLOBIN)


Mass: 17399.180 Da / Num. of mol.: 1 / Mutation: L104F, 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


Mass: 96.063 Da / Num. of mol.: 1 / 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.: 140 / 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: 3.08 Å3/Da / Density % sol: 61.49 %
Crystal growpH: 9
Details: 2.6-3.0 M AMMONIUM SULFATE, 20 MM TRIS, 1 MM EDTA, PH 9.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
22.4-3.0 Mammonium sulfate1drop
320 mMTris-HCl1drop
41 mMEDTA1drop
52.4-3.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 25279 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.083
Reflection
*PLUS
Num. obs: 12814 / Num. measured all: 66964

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.851model building
SHELXL-97model building
SHELXL-97refinement
XDSdata reduction
X-PLOR3.851phasing
SHELXL-97phasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1MBW

1mbw
PDB Unreleased entry


Resolution: 2.1→5 Å / Num. parameters: 5700 / Num. restraintsaints: 5461 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 1181 11.1 %RANDOM
all0.1466 10633 --
obs0.1506 -88.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1424.3
Refinement stepCycle: LAST / Resolution: 2.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 49 139 1416
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0.005
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.08
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.087
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.147 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.9
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg21
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.4
X-RAY DIFFRACTIONs_chiral_restr0.037

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