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- PDB-1s56: Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 1s56
TitleCrystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Xe Atoms
ComponentsHemoglobin-like protein HbN
KeywordsOXYGEN STORAGE/TRANSPORT / GROUP I TRUNCATED HEMOGLOBIN / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


detoxification of nitrogen compound / Tolerance by Mtb to nitric oxide produced by macrophages / nitric oxide dioxygenase NAD(P)H activity / nitric oxide catabolic process / thioredoxin peroxidase activity / cell redox homeostasis / oxygen carrier activity / oxygen binding / cellular response to oxidative stress / heme binding ...detoxification of nitrogen compound / Tolerance by Mtb to nitric oxide produced by macrophages / nitric oxide dioxygenase NAD(P)H activity / nitric oxide catabolic process / thioredoxin peroxidase activity / cell redox homeostasis / oxygen carrier activity / oxygen binding / cellular response to oxidative stress / heme binding / metal ion binding / cytoplasm / cytosol
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 / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / PHOSPHATE ION / XENON / Group 1 truncated hemoglobin GlbN / Group 1 truncated hemoglobin GlbN
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsMilani, M. / Pesce, A. / Ouellet, Y. / Dewilde, S. / Friedman, J. / Ascenzi, P. / Guertin, M. / Bolognesi, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Heme-ligand tunneling in group I truncated hemoglobins
Authors: Milani, M. / Pesce, A. / Ouellet, Y. / Dewilde, S. / Friedman, J. / Ascenzi, P. / Guertin, M. / Bolognesi, M.
History
DepositionJan 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / 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_asym_id / _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.ptnr2_auth_asym_id / _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_asym_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_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin-like protein HbN
B: Hemoglobin-like protein HbN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,40016
Polymers28,9292
Non-polymers2,47114
Water1,928107
1
A: Hemoglobin-like protein HbN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6738
Polymers14,4651
Non-polymers1,2097
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemoglobin-like protein HbN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7278
Polymers14,4651
Non-polymers1,2637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.321, 61.959, 90.747
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, 2 molecules AB

#1: Protein Hemoglobin-like protein HbN / Flavohemoglobin


Mass: 14464.515 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: GLBN, RV1542C, MT1594, MTCY48.23, MB1569C / Production host: Escherichia coli (E. coli) / References: UniProt: P0A592, UniProt: P9WN25*PLUS

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Non-polymers , 7 types, 121 molecules

#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Xe
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.15 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: phosphate, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 22, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. all: 9301 / Num. obs: 9301 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.098 / Net I/σ(I): 6.9
Reflection shellResolution: 2.43→2.56 Å / Redundancy: 4 % / Rsym value: 0.277 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1RTE

1rte


Resolution: 2.43→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.732 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27692 447 4.8 %RANDOM
Rwork0.19435 ---
all0.19816 8854 --
obs0.19816 8854 94.25 %-
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: 29.003 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.43→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 104 107 2179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212104
X-RAY DIFFRACTIONr_bond_other_d00.021927
X-RAY DIFFRACTIONr_angle_refined_deg1.2242.092880
X-RAY DIFFRACTIONr_angle_other_deg3.63634445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1055261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022332
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02400
X-RAY DIFFRACTIONr_nbd_refined0.330.2698
X-RAY DIFFRACTIONr_nbd_other0.3010.22361
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1120.21026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.140.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3760.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3991.51300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74122078
X-RAY DIFFRACTIONr_scbond_it1.0313804
X-RAY DIFFRACTIONr_scangle_it1.7414.5802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.433→2.496 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 30
Rwork0.258 583

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