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- PDB-2qrw: Crystal structure of Mycobacterium tuberculosis trHbO WG8F mutant -

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Basic information

Entry
Database: PDB / ID: 2qrw
TitleCrystal structure of Mycobacterium tuberculosis trHbO WG8F mutant
ComponentsHemoglobin-like protein HbO
KeywordsTRANSPORT PROTEIN / truncated hemoglobin fold / alpha helix / Heme / Hydroxylation / Iron / Membrane / Metal-binding / Oxygen transport / Transport
Function / homology
Function and homology information


oxygen transport / oxygen carrier activity / oxygen binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Two-on-two hemoglobin-3 / 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 / PROTOPORPHYRIN IX CONTAINING FE / Group 2 truncated hemoglobin GlbO / Group 2 truncated hemoglobin GlbO
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsMilani, M. / Bolognesi, M.
CitationJournal: Biochemistry / Year: 2007
Title: The Roles of Tyr(CD1) and Trp(G8) in Mycobacterium tuberculosis Truncated Hemoglobin O in Ligand Binding and on the Heme Distal Site Architecture
Authors: Ouellet, H. / Milani, M. / LaBarre, M. / Bolognesi, M. / Couture, M. / Guertin, M.
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2016Group: Structure summary
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin-like protein HbO
B: Hemoglobin-like protein HbO
C: Hemoglobin-like protein HbO
D: Hemoglobin-like protein HbO
E: Hemoglobin-like protein HbO
F: Hemoglobin-like protein HbO
G: Hemoglobin-like protein HbO
H: Hemoglobin-like protein HbO
I: Hemoglobin-like protein HbO
J: Hemoglobin-like protein HbO
K: Hemoglobin-like protein HbO
L: Hemoglobin-like protein HbO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,11359
Polymers179,19412
Non-polymers9,91947
Water30,5531696
1
B: Hemoglobin-like protein HbO
H: Hemoglobin-like protein HbO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,53510
Polymers29,8662
Non-polymers1,6698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
MethodPISA
2
A: Hemoglobin-like protein HbO
G: Hemoglobin-like protein HbO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,72712
Polymers29,8662
Non-polymers1,86110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
MethodPISA
3
C: Hemoglobin-like protein HbO
I: Hemoglobin-like protein HbO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2477
Polymers29,8662
Non-polymers1,3815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
MethodPISA
4
D: Hemoglobin-like protein HbO
L: Hemoglobin-like protein HbO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,63111
Polymers29,8662
Non-polymers1,7659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
MethodPISA
5
E: Hemoglobin-like protein HbO
J: Hemoglobin-like protein HbO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4399
Polymers29,8662
Non-polymers1,5737
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
MethodPISA
6
F: Hemoglobin-like protein HbO
K: Hemoglobin-like protein HbO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,53510
Polymers29,8662
Non-polymers1,6698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
MethodPISA
7
B: Hemoglobin-like protein HbO
E: Hemoglobin-like protein HbO
H: Hemoglobin-like protein HbO
J: Hemoglobin-like protein HbO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,97419
Polymers59,7314
Non-polymers3,24215
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10950 Å2
MethodPISA
8
A: Hemoglobin-like protein HbO
D: Hemoglobin-like protein HbO
G: Hemoglobin-like protein HbO
L: Hemoglobin-like protein HbO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,35823
Polymers59,7314
Non-polymers3,62719
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
MethodPISA
9
C: Hemoglobin-like protein HbO
F: Hemoglobin-like protein HbO
I: Hemoglobin-like protein HbO
K: Hemoglobin-like protein HbO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,78217
Polymers59,7314
Non-polymers3,05013
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.312, 187.312, 274.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein
Hemoglobin-like protein HbO / Truncated hemoglobin / trHbO


Mass: 14932.825 Da / Num. of mol.: 12 / Mutation: W88F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glbO / Production host: Escherichia coli (E. coli) / References: UniProt: P0A595, UniProt: P9WN23*PLUS
#2: Chemical
ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CN
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1696 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 2.2 M ammonium sulfate, 0.05 M phosphate buffer, 0.001 M KCN, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorDetector: CCD / Date: Oct 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.93→47.67 Å / Num. obs: 178559 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.7
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.3 / Num. unique all: 23850 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ngk
Resolution: 1.93→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21475 8925 5 %RANDOM
Rwork0.17557 ---
all0.17752 169584 --
obs0.17752 169584 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.513 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.93→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12462 0 655 1696 14813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02113658
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1362.07818640
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.76651554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.40521.717728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13152166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.55915187
X-RAY DIFFRACTIONr_chiral_restr0.0810.21795
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210865
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.19295
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.12405
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.148
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.00927713
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.511312374
X-RAY DIFFRACTIONr_scbond_it7.07945945
X-RAY DIFFRACTIONr_scangle_it9.59366261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 543 -
Rwork0.261 10538 -
obs--83.74 %

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