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- PDB-1ngk: Crystallographic Structure of Mycobacterium tuberculosis Hemoglobin O -

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Basic information

Entry
Database: PDB / ID: 1ngk
TitleCrystallographic Structure of Mycobacterium tuberculosis Hemoglobin O
ComponentsHemoglobin-like protein HbO
KeywordsOXYGEN STORAGE/TRANSPORT / TRUNCATED HEMOGLOBIN / OXYGEN STORAGE-TRANSPORT COMPLEX
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 / MAD / Resolution: 2.11 Å
AuthorsMilani, M. / Savard, P.-Y. / Oullet, H. / Ascenzi, P. / Guertin, M. / Bolognesi, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: A TyrCD1/TrpG8 hydrogen bond network and a TyrB10-TyrCD1 covalent link shape the heme distal site of Mycobacterium tuberculosis hemoglobin O
Authors: Milani, M. / Savard, P.-Y. / Oullet, H. / Ascenzi, P. / Guertin, M. / Bolognesi, M.
History
DepositionDec 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)189,10254
Polymers179,66212
Non-polymers9,43942
Water29,1481618
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45120 Å2
ΔGint-600 kcal/mol
Surface area62920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.034, 187.034, 274.861
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


Mass: 14971.860 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A595, UniProt: P9WN23*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CN
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 1618 / 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: 2.84 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: ammonium sulphate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113.5 mg/mlprotein1drop
22.15 Mammonium sulfate1reservoir
30.001 M1reservoirKCN
40.05 Mphosphate1reservoirpH7.25

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONEMBL/DESY, Hamburg BW7B10.84
SYNCHROTRONESRF ID2921.7387
SYNCHROTRONESRF ID2931.7404
SYNCHROTRONESRF ID2940.9801
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATEAug 7, 2001
MARRESEARCH2CCDFeb 21, 2002
MARRESEARCH3CCDFeb 21, 2002
MARRESEARCH4CCDFeb 21, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Triangular monochromatorSINGLE WAVELENGTHMx-ray1
2channel - cut Si monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.841
21.73871
31.74041
40.98011
ReflectionResolution: 2.11→50 Å / Num. all: 131238 / Num. obs: 131238 / % possible obs: 99.67 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.8 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 138692 / % possible obs: 99.7 % / Redundancy: 11 % / Num. measured all: 1533455
Reflection shell
*PLUS
% possible obs: 97.5 % / Redundancy: 3 %

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.11→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22586 6934 5 %RANDOM
Rwork0.18567 ---
all0.18768 131238 --
obs0.18768 131238 99.67 %-
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: 25.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12856 0 630 1618 15104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02113599
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.252.06618590
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.56551561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.21810
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210808
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.21473
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.072.57796
X-RAY DIFFRACTIONr_mcangle_it1.985412457
X-RAY DIFFRACTIONr_scbond_it2.5314.55803
X-RAY DIFFRACTIONr_scangle_it3.60866133
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 508
Rwork0.219 9483
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.25

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