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- PDB-1emy: CRYSTAL STRUCTURE OF ASIAN ELEPHANT (ELEPHAS MAXIMUS) CYANO-MET M... -

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Basic information

Entry
Database: PDB / ID: 1emy
TitleCRYSTAL STRUCTURE OF ASIAN ELEPHANT (ELEPHAS MAXIMUS) CYANO-MET MYOGLOBIN AT 1.78 ANGSTROMS RESOLUTION. PHE 29 (B10) ACCOUNTS FOR ITS UNUSUAL LIGAND BINDING PROPERTIES
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / HEME PROTEIN / GLOBIN FOLD
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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesElephas maximus (Asiatic elephant)
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
AuthorsBisig, D.A. / Piontek, K.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Crystal structure of Asian elephant (Elephas maximus) cyano-metmyoglobin at 1.78-A resolution. Phe29(B10) accounts for its unusual ligand binding properties.
Authors: Bisig, D.A. / Di Iorio, E.E. / Diederichs, K. / Winterhalter, K.H. / Piontek, K.
#1: Journal: To be Published
Title: A Double Mutant of Sperm Whale Myoglobin Mimics the Structure and Function of Elephant Myoglobin
Authors: Zhao, X. / Vyas, K. / Nguyen, B.D. / Rajarathnam, K. / La Mar, G.N. / Li, T. / Phillips Jr., G.N. / Eich, R.F. / Olson, J.S. / Ling, J. / Bocian, D.F.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: 1H NMR Investigation of the Heme Cavity of Elephant (E7 Gln) met-Cyano-Myoglobin. Evidence for a B-Helix Phenylalanine Interaction with Bound Ligand
Authors: Vyas, K. / Rajarathnam, K. / Yu, L.P. / Emerson, S.D. / La Mar, G.N. / Krishnamoorthi, R.
History
DepositionFeb 22, 1995Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Downloads & links

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Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6693
Polymers17,0271
Non-polymers6432
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.510, 58.590, 70.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MYOGLOBIN


Mass: 17026.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elephas maximus (Asiatic elephant) / Organ: SKELETAL / References: UniProt: P02186
#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#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.: 219 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND MET FORM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growDetails: CRYSTALLIZATION CONDITIONS METHOD: HANGING DROP VAPOR DIFFUSION PRECIPITANT: 45% PEG 1000 BUFFER: 0.1M TRIS/HCL PH: 8.5 SALT: 0.15M MAGNESIUM ACETATE PROTEIN CONCENTRATION: 10MG/ML ...Details: CRYSTALLIZATION CONDITIONS METHOD: HANGING DROP VAPOR DIFFUSION PRECIPITANT: 45% PEG 1000 BUFFER: 0.1M TRIS/HCL PH: 8.5 SALT: 0.15M MAGNESIUM ACETATE PROTEIN CONCENTRATION: 10MG/ML TEMPERATURE: 293K CRYSTAL SIZE: 0.8 X 0.4 X 0.3 MM
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
245 %PEG10001reservoir
3100 mMTris-HCl1reservoir
4150 mMmagnesium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 13649 / % possible obs: 93.6 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 1.78 Å / Redundancy: 5 % / Num. measured all: 68768 / Rmerge(I) obs: 0.045

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.78→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.153 -
obs0.153 12966
Displacement parametersBiso mean: 21.45 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.78→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 45 219 1466
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.8011
X-RAY DIFFRACTIONx_mcangle_it2.5791.5
X-RAY DIFFRACTIONx_scbond_it3.5021
X-RAY DIFFRACTIONx_scangle_it5.5181.5
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.040.039
X-RAY DIFFRACTIONx_planar_d0.050.051
X-RAY DIFFRACTIONx_plane_restr0.020.017
X-RAY DIFFRACTIONx_chiral_restr0.150.148

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