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- PDB-2hz1: The x-ray crystal structure of ferrous Synechocystis hemoglobin w... -

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Basic information

Entry
Database: PDB / ID: 2hz1
TitleThe x-ray crystal structure of ferrous Synechocystis hemoglobin with a covalent linkage
ComponentsCyanoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / Synechocystis / hemoglobin / heme / globin / ferrous / hexacoordinate / covalent heme vinyl link / 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 / SULFUR DIOXIDE / SULFITE ION / Group 1 truncated hemoglobin GlbN
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHoy, J.A.
CitationJournal: Protein Sci. / Year: 2007
Title: Covalent heme attachment in Synechocystis hemoglobin is required to prevent ferrous heme dissociation
Authors: Hoy, J.A. / Smagghe, B.J. / Halder, P. / Hargrove, M.S.
History
DepositionAug 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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 / 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_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.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.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_conn_type.id / _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)14,8077
Polymers13,7571
Non-polymers1,0506
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.662, 46.503, 62.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P73925

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Non-polymers , 5 types, 136 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 31% PEG MME 5000, 0.1 M MES, 0.2 M ammonium sulfate, 0.01 M cadmium chloride, 0.01 M sodium hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→37.27 Å / Num. all: 11443 / Num. obs: 11435 / % possible obs: 99.93 % / Redundancy: 6.83 % / Rmerge(I) obs: 0.046 / Rsym value: 0.248
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.68 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 9.6 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1RTX

1rtx


Resolution: 1.8→37.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.856 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 598 5 %RANDOM
Rwork0.18875 ---
all0.1912 11443 --
obs0.19117 11435 99.93 %-
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: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.73 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 55 130 1154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211044
X-RAY DIFFRACTIONr_bond_other_d0.0020.02908
X-RAY DIFFRACTIONr_angle_refined_deg1.5962.0111417
X-RAY DIFFRACTIONr_angle_other_deg0.95832100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3455122
X-RAY DIFFRACTIONr_chiral_restr0.10.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021192
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02221
X-RAY DIFFRACTIONr_nbd_refined0.2560.2308
X-RAY DIFFRACTIONr_nbd_other0.2380.21095
X-RAY DIFFRACTIONr_nbtor_other0.0910.2529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.290
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.214
X-RAY DIFFRACTIONr_mcbond_it0.9461.5608
X-RAY DIFFRACTIONr_mcangle_it1.7232962
X-RAY DIFFRACTIONr_scbond_it2.713436
X-RAY DIFFRACTIONr_scangle_it4.1814.5455
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 44
Rwork0.251 823

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