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- PDB-1mwb: Solution structure of the recombinant hemoglobin from the cyanoba... -

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Basic information

Entry
Database: PDB / ID: 1mwb
TitleSolution structure of the recombinant hemoglobin from the cyanobacterium Synechocystis sp. PCC 6803 in its hemichrome state
ComponentsCyanoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / globin / cyanoglobin / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


thioredoxin peroxidase activity / cell redox homeostasis / oxygen carrier activity / oxygen binding / cellular response to oxidative stress / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Truncated hemoglobin, group 1 / Globin, bacterial-like, conserved site / Protozoan/cyanobacterial globins signature. / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Group 1 truncated hemoglobin GlbN
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsional angle database
AuthorsFalzone, C.J. / Vu, B.C. / Scott, N.L. / Lecomte, J.T.
Citation
Journal: J.MOL.BIOL. / Year: 2002
Title: The Solution Structure of the Recombinant Hemoglobin from the Cyanobacterium Synechocystis sp. PCC 6803 in its Hemichrome State
Authors: Falzone, C.J. / Vu, B.C. / Scott, N.L. / Lecomte, J.T.
#1: Journal: J.Biomol.NMR / Year: 2002
Title: Assignment of the 1H, 13C, and 15N Signals of Synechocystis sp. PCC 6803 Methemoglobin
Authors: Falzone, C.J. / Lecomte, J.T.
#2: Journal: Protein Sci. / Year: 2000
Title: Cloning, Expression, Purification, and Preliminary Characterization of a Putative Hemoglobin from the Cyanobacterium Synechocystis sp. PCC 6803
Authors: Scott, N.L. / Lecomte, J.T.
History
DepositionSep 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Remark 999SEQUENCE AUTHORS INFORMED THAT MET 1 IN SWISSPROT P73925 WAS CLEAVED POST-TRANSLATIONALLY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3742
Polymers13,7571
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with lowest energy and least restraint violations
RepresentativeModel #1lowest energy and fewest violations

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Components

#1: Protein Cyanoglobin / Hemoglobin / Hb


Mass: 13757.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: slr2097 (glbN) / Plasmid: pET3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P73925
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1243D 13C-separated NOESY
1333D 15N-separated NOESY
143J-MODULATED 1H-15N HSQC
1522D TOCSY
NMR detailsText: This is a low-spin Fe(+3) complex. Standard methods as applied to dimagnetic proteins were used to determine the structure.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 - 2 mM protein, 20 mM K or Na phosphate90% H2O/10% D2O
20.6 - 2 mM protein, 20 mM K or Na phosphate100% D2O
31 mM U-15N protein, 20 mM K or Na phosphate90% H2O/10% D2O
41 mM U-15N, 13C protein, 20 mM K or Na phosphate90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM / pH: 7.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
Felix2000Accelrysdata analysis
XwinNMR2.5Brukercollection
NMRPipe2.1Delaglioprocessing
X-PLOR-NIH1.2.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsional angle database
Software ordinal: 1
NMR representativeSelection criteria: lowest energy and fewest violations
NMR ensembleConformer selection criteria: structures with lowest energy and least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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