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- PDB-1s69: The X-ray structure of the cyanobacteria Synechocystis hemoglobin... -

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Basic information

Entry
Database: PDB / ID: 1s69
TitleThe X-ray structure of the cyanobacteria Synechocystis hemoglobin "cyanoglobin" with cyanide ligand
ComponentsCyanoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / 2 on 2 helical fold / globin / heme / iron / hemoglobin / cyanobacteria / oxygen binding / hexacoordinate / truncated / 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
CYANIDE ION / CITRATE ANION / PROTOPORPHYRIN IX CONTAINING FE / Group 1 truncated hemoglobin GlbN
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsTrent III, J.T. / Kundu, S. / Hoy, J.A. / Hargrove, M.S.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystallographic analysis of synechocystis cyanoglobin reveals the structural changes accompanying ligand binding in a hexacoordinate hemoglobin.
Authors: Trent III, J.T. / Kundu, S. / Hoy, J.A. / Hargrove, M.S.
History
DepositionJan 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,7204
Polymers13,8891
Non-polymers8323
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.060, 84.060, 64.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Cyanoglobin / Hemoglobin / Hb


Mass: 13888.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: GLBN, SLR2097 / Plasmid: pET28c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P73925
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 68.77 % / Description: Friedel pairs were used.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5M sodium citrate, 0.2M ammonium citrate, 20% sucrose, 3% dioxane, 25mM sodium cyanide, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEOct 1, 2002
RIGAKU RAXIS IV2IMAGE PLATEOct 2, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→32.49 Å / Num. obs: 37950 / % possible obs: 75.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.92 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.3
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 1.02 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.1 / Num. unique all: 254 / % possible all: 5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CRYSTALVIEWdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1dly

1dly


Resolution: 1.68→32.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.564 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.099 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Friedel pairs were used.
RfactorNum. reflection% reflectionSelection details
Rfree0.19921 1053 5.1 %RANDOM
Rwork0.19236 ---
all0.19921 ---
obs0.1927 37837 80.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.68→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 58 148 1175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0211050
X-RAY DIFFRACTIONr_angle_refined_deg1.8092.0881429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2945122
X-RAY DIFFRACTIONr_chiral_restr0.1210.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02820
X-RAY DIFFRACTIONr_nbd_refined0.2290.2547
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.217
X-RAY DIFFRACTIONr_mcbond_it1.0191.5610
X-RAY DIFFRACTIONr_mcangle_it1.9272967
X-RAY DIFFRACTIONr_scbond_it3.4423440
X-RAY DIFFRACTIONr_scangle_it5.6584.5462
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.457 9
Rwork0.437 121

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