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- PDB-1a7e: HYDROXOMET MYOHEMERYTHRIN FROM THEMISTE ZOSTERICOLA -

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Basic information

Entry
Database: PDB / ID: 1a7e
TitleHYDROXOMET MYOHEMERYTHRIN FROM THEMISTE ZOSTERICOLA
ComponentsMYOHEMERYTHRIN
KeywordsOXYGEN TRANSPORT / NONHEME IRON OXYGEN CARRIER
Function / homology
Function and homology information


inorganic ion homeostasis / monoatomic cation homeostasis / oxygen carrier activity / iron ion binding
Similarity search - Function
Haemerythrin / Hemerythrin-like / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HYDROXY DIIRON-OXO MOIETY / Myohemerythrin
Similarity search - Component
Biological speciesThemiste zostericola (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsMartins, L.J. / Hill, C.P. / Ellis Junior, W.R.
CitationJournal: Biochemistry / Year: 1997
Title: Structures of wild-type chloromet and L103N hydroxomet Themiste zostericola myohemerythrins at 1.8 A resolution.
Authors: Martins, L.J. / Hill, C.P. / Ellis Jr., W.R.
History
DepositionMar 12, 1998Processing site: BNL
Revision 1.0Oct 14, 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 / pdbx_struct_conn_angle / 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 / _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.ptnr2_label_atom_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_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 7, 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: MYOHEMERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0174
Polymers13,8021
Non-polymers2163
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.885, 81.170, 36.685
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 MYOHEMERYTHRIN


Mass: 13801.691 Da / Num. of mol.: 1 / Mutation: L103N
Source method: isolated from a genetically manipulated source
Details: CONTAINS A HYDROXY-DIIRON-OXO (FE1-O-FE2) MOIETY (CFO).
Source: (gene. exp.) Themiste zostericola (invertebrata) / Tissue: RETRACTOR MUSCLES / Cell line: BL21 / Plasmid: PL103N / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P02247
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-OFO / HYDROXY DIIRON-OXO MOIETY


Mass: 144.697 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2HO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growpH: 7 / Details: 27% PEG 6K, 100MM HEPES, 1.0M LICL (PH 7.0)
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
127 %(v/v)PEG60001reservoir
20.1 MHEPES1reservoir
31.0 M1reservoirLiClpH7.0
40.05 MTris-HCl1drop
50.2 M1dropKClpH8.0

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Data collection

DiffractionMean temperature: 119 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1988
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→10 Å / Num. obs: 11853 / % possible obs: 88.2 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.07
Reflection
*PLUS
Num. measured all: 102018
Reflection shell
*PLUS
Highest resolution: 1.74 Å / Lowest resolution: 1.8 Å / % possible obs: 49.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.8phasing
RefinementResolution: 1.8→10 Å / Rfactor Rfree error: 0.007 / 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
Rfree0.227 1087 10.3 %RANDOM
Rwork0.186 ---
obs0.186 10508 87.3 %-
Displacement parametersBiso mean: 11.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-10 Å
Luzzati sigma a0.03 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 6 204 1183
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg2.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.761.5
X-RAY DIFFRACTIONx_mcangle_it1.112
X-RAY DIFFRACTIONx_scbond_it1.712
X-RAY DIFFRACTIONx_scangle_it2.682.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.283 69 9.2 %
Rwork0.236 680 -
obs--63.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46

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