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- PDB-1rtx: Crystal Structure of Synechocystis Hemoglobin with a Covalent Hem... -

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Basic information

Entry
Database: PDB / ID: 1rtx
TitleCrystal Structure of Synechocystis Hemoglobin with a Covalent Heme Linkage
ComponentsCyanoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / Synechocystis hemoglobin / hexacoordinate / hemichrome / 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
: / PROTOPORPHYRIN IX CONTAINING FE / : / Group 1 truncated hemoglobin GlbN
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsHoy, J.A. / Kundu, S. / Trent, J.T. / Ramaswamy, S. / Hargrove, M.S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The crystal structure of synechocystis hemoglobin with a covalent heme linkage.
Authors: Hoy, J.A. / Kundu, S. / Trent, J.T. / Ramaswamy, S. / Hargrove, M.S.
History
DepositionDec 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Cyanoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7346
Polymers13,7571
Non-polymers9765
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.500, 46.000, 61.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological unit is a monomer, four in the asymmetric unit.

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Components

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Protein , 1 types, 1 molecules A

#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: GLBN, SLR2097 / Plasmid: pet28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P73925

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Non-polymers , 5 types, 84 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG MME 5000, 0.2M ammonium sulfate, 0.01 cadmium chloride, 0.1M MES, 0.01M potassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)Wavelength
SYNCHROTRONSSRL BL1-511.737570, 1.239793, 1.739925
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDDec 3, 20021M RH COATED BENT CYLINDRICAL M
RIGAKU RAXIS IV2IMAGE PLATEJan 20, 2002Osmic confocal
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
12-CRYSTAL, SI111MADMx-ray1
2NULLSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.737571
21.2397931
31.7399251
41.54181
ReflectionResolution: 1.8→36.76 Å / Num. all: 10922 / Num. obs: 10617 / % possible obs: 97.2 % / Rmerge(I) obs: 0.048
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.211 / % possible all: 78.8

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Processing

Software
NameVersionClassification
d*TREKdata scaling
d*TREKdata reduction
REFMAC5.1.24refinement
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→36.76 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.134 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 649 5.8 %RANDOM
Rwork0.218 ---
all0.218 10922 --
obs0.218 10617 97.2 %-
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: 33.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---1.45 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 51 79 1099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211043
X-RAY DIFFRACTIONr_angle_refined_deg3.9562.0121419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745122
X-RAY DIFFRACTIONr_chiral_restr0.0950.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02830
X-RAY DIFFRACTIONr_nbd_refined0.2420.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.29
X-RAY DIFFRACTIONr_mcbond_it0.8231.5608
X-RAY DIFFRACTIONr_mcangle_it1.4692962
X-RAY DIFFRACTIONr_scbond_it2.3123435
X-RAY DIFFRACTIONr_scangle_it3.5824.5457
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 35 -
Rwork0.252 645 -
obs-645 78.8 %

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