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- PDB-1vrf: SOLUTION STRUCTURE OF COMPONENT IV GLYCERA DIBRANCHIATA MONOMERIC... -

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Basic information

Entry
Database: PDB / ID: 1vrf
TitleSOLUTION STRUCTURE OF COMPONENT IV GLYCERA DIBRANCHIATA MONOMERIC HEMOGLOBIN-CO
ComponentsPROTEIN (GLOBIN, MONOMERIC COMPONENT M-IV)
KeywordsHEME PROTEIN / GLOBIN / OXYGEN TRANSPORT
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Globin, monomeric component M-IV
Similarity search - Component
Biological speciesGlycera dibranchiata (invertebrata)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsVolkman, B.F. / Alam, S.L. / Satterlee, J.D. / Markley, J.L.
Citation
Journal: Biochemistry / Year: 1998
Title: Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO.
Authors: Volkman, B.F. / Alam, S.L. / Satterlee, J.D. / Markley, J.L.
#1: Journal: J.Biomol.Nmr / Year: 1998
Title: Detailed NMR analysis of the heme-protein interactions in component IV Glycera dibranchiata monomeric hemoglobin-CO.
Authors: Alam, S.L. / Volkman, B.F. / Markley, J.L. / Satterlee, J.D.
History
DepositionMar 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 1, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 13, 2019Group: Atomic model / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_abbrev / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (GLOBIN, MONOMERIC COMPONENT M-IV)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6943
Polymers15,0491
Non-polymers6442
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1250 Å2
ΔGint-19 kcal/mol
Surface area6910 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1
Representative

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Components

#1: Protein PROTEIN (GLOBIN, MONOMERIC COMPONENT M-IV) / GHM4


Mass: 15049.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycera dibranchiata (invertebrata) / Tissue: BLOOD / Description: RECOMBINANT PROTEIN WAS PRODUCED IN E. COLI / Cell: ERYTHROCYTE / Plasmid: PET9D / Production host: Escherichia coli (E. coli) / References: UniProt: P15447
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOEY & QUANTITATIVE J-CORRELATION
NMR detailsText: 3D 15N NOESY-HSQC; 3D 13C NOESY-HSQC; 4D 13C/15N NOESY-HSQC; 3D HNHB; 3D HNCOHB; 2D JCC; 2D JNC; 3D HNHA; 2D LRCC

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM KCL / pH: 5.0 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX499.841
Bruker DMXBrukerDMX500.132
Bruker DMXBrukerDMX600.133
Bruker DMXBrukerDMX750.134

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.843BRUNGERrefinement
X-PLOR3.843structure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINED ITERATIVELY WITH X-PLOR AND PERL SCRIPTS WRITTEN IN-HOUSE AS DESCRIBED IN JRNL CITATION ABOVE
NMR ensembleConformers calculated total number: 1 / Conformers submitted total number: 1

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