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- PDB-2mhr: STRUCTURE OF MYOHEMERYTHRIN IN THE AZIDOMET STATE AT 1.7(SLASH)1.... -

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Entry
Database: PDB / ID: 2mhr
TitleSTRUCTURE OF MYOHEMERYTHRIN IN THE AZIDOMET STATE AT 1.7(SLASH)1.3 ANGSTROMS RESOLUTION
ComponentsMYOHEMERYTHRIN
KeywordsOXYGEN BINDING
Function / homology
Function and homology information


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) ...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
AZIDE ION / MU-OXO-DIIRON / Myohemerythrin
Similarity search - Component
Biological speciesThemiste zostericola (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 1.3 Å
AuthorsSheriff, S. / Hendrickson, W.A.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Structure of myohemerythrin in the azidomet state at 1.7/1.3 A resolution.
Authors: Sheriff, S. / Hendrickson, W.A. / Smith, J.L.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1987
Title: Location of Iron and Sulfur Atoms in Myohemerythrin from Anomalous-Scattering Measurements
Authors: Sheriff, S. / Hendrickson, W.A.
#2: Journal: Acta Crystallogr.,Sect.A / Year: 1987
Title: General Density Function Corresponding to X-Ray Diffraction with Anomalous Scattering Included
Authors: Hendrickson, W.A. / Sheriff, S.
#3: Journal: Acta Crystallogr.,Sect.A / Year: 1987
Title: Description of Overall Anisotropy in Diffraction from Macromolecular Crystals
Authors: Sheriff, S. / Hendrickson, W.A.
#4: Journal: Biochemistry / Year: 1986
Title: Structural Heterogeneity in Protein Crystals
Authors: Smith, J.L. / Hendrickson, W.A. / Honzatko, R.B. / Sheriff, S.
#5: Journal: Biomolecular Stereodynamics III. Proceedings of the Fourth Conversation in the Discipline of Biomolecular Stereodynamics
Year: 1986
Title: Mobility and Heterogeneity in Protein Structure as Seen by Diffraction
Authors: Hendrickson, W.A. / Smith, J.L. / Sheriff, S.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: Influence of Solvent Accessibility and Intermolecular Contacts on Atomic Mobilities in Hemerythrins
Authors: Sheriff, S. / Hendrickson, W.A. / Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H.
#7: Journal: Respiratory Pigments in Animals / Year: 1985
Title: Structure and Function of Hemerythrins
Authors: Hendrickson, W.A. / Smith, J.L. / Sheriff, S.
#8: Journal: Life Chem.Rep.,Suppl.Ser. / Year: 1983
Title: Structure of the Active Center of Hemerythrins
Authors: Sheriff, S. / Hendrickson, W.A. / Smith, J.L.
#9: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975
Title: Tertiary Structure of Myohemerythrin at Low Resolution
Authors: Hendrickson, W.A. / Klippenstein, G.L. / Ward, K.B.
History
DepositionApr 20, 1987Processing site: BNL
Revision 1.0Oct 16, 1987Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
SupersessionNov 25, 2008ID: 1MHR
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_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

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Assembly

Deposited unit
A: MYOHEMERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2596
Polymers13,8011
Non-polymers4585
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.660, 80.170, 37.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO 7 AND PRO 90 ARE CIS PROLINES.

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Components

#1: Protein MYOHEMERYTHRIN


Mass: 13800.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Themiste zostericola (invertebrata) / References: UniProt: P02247
#2: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE ARE TWO TURNS IN MYOHEMERYTHRIN WHICH INVOLVE A QUINTET OF RESIDUES AND ARE NOT WELL ...THERE ARE TWO TURNS IN MYOHEMERYTHRIN WHICH INVOLVE A QUINTET OF RESIDUES AND ARE NOT WELL DESCRIBED BY PREVIOUS CATEGORIZATION. THE FIRST SUCH TURN IS FROM ARG 15 TO GLU 19. PHE 17 IS IN A LEFT-HANDED ALPHA CONFORMATION. SIDE CHAIN TO MAIN CHAIN HYDROGEN BONDS ARE RESPONSIBLE FOR STABILIZING THIS STRUCTURE. THESE INCLUDE N VAL 16 - OD2 ASP 22, N PHE 17 - OD1 ASP 22, OH TYR 18 - N GLY 116 AND OH TYR 18 - N LEU 118. THE SECOND TURN IS FROM ARG 37 TO ALA 41 (INCLUDING THE INVERSE GAMMA BEND, TURN 4 BELOW). THIS IS ALSO STABILIZED BY SIDE CHAIN TO MAIN CHAIN HYDROGEN BONDING INCLUDING ND2 ASN 43 - O ASP 38, N ASN 43 - OG SER 40. THE LATTER HYDROGEN BOND (SIDE CHAIN TO NH(N+3)) IS COMMON AT THE BEGINNING OF ALPHA-HELICES. ALSO HOH 139 LINKS O SER 40 WITH OD1 ASN 39 AND HOH 148 LINKS OD1 ASP 38 WITH OG SER 40. TURN 6 IS PART OF A LARGER END-OF-HELIX STRUCTURE FIRST DESCRIBED BY C. SCHELLMAN (1980) IN *PROTEIN FOLDING* (R.JAENICKE, ED.), PP. 53-61, ELSEVIER, AMSTERDAM. IT ALSO INCLUDES A HYDROGEN BOND FROM O MET 62 TO N TYR 67 AND WHICH REQUIRES THE N-1 RESIDUE (LYS 66) TO BE IN A LEFT-HANDED ALPHA-HELICAL CONFORMATION.
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal grow
*PLUS
pH: 6.7 / Method: unknown / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
155 %satammonium sulfate11
20.1 Mcacodylic acid11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.3→10 Å / Rfactor obs: 0.158 / σ(F): 4
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.82 Å2--
2---9.1 Å2-
3---3.28 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 21 157 2177
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0140.02
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1660.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Num. reflection obs: 16654 / σ(I): 2 / Highest resolution: 1.3 Å / Lowest resolution: 1.7 Å / Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS

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