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- PDB-5v3v: Crystal Structure of the Group II Truncated Hemoglobin from Bacil... -

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Basic information

Entry
Database: PDB / ID: 5v3v
TitleCrystal Structure of the Group II Truncated Hemoglobin from Bacillus Anthracis: Tyr26Ala Mutant
ComponentsGlobin
KeywordsOXYGEN TRANSPORT / truncated hemoglobin / heme protein
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
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 / Protozoan/cyanobacterial globin family protein / Protozoan/cyanobacterial globin family protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.14 Å
AuthorsVarnado, C.L. / SoRelle, E. / Soman, J. / Olson, J.S.
CitationJournal: To Be Published
Title: Crystal Structure of the Group II Truncated Hemoglobin from Bacillus Anthracis
Authors: Varnado, C.L. / SoRelle, E. / Soman, J. / Olson, J.S.
History
DepositionMar 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Globin
B: Globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6319
Polymers30,0582
Non-polymers1,5737
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-96 kcal/mol
Surface area12170 Å2
MethodPISA
2
A: Globin
B: Globin
hetero molecules

A: Globin
B: Globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,26218
Polymers60,1164
Non-polymers3,14614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area11470 Å2
ΔGint-218 kcal/mol
Surface area23140 Å2
MethodPISA
3
B: Globin
hetero molecules

B: Globin
hetero molecules

A: Globin
hetero molecules

A: Globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,26218
Polymers60,1164
Non-polymers3,14614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
Buried area10540 Å2
ΔGint-201 kcal/mol
Surface area24070 Å2
MethodPISA
4
A: Globin
B: Globin
hetero molecules

A: Globin
B: Globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,26218
Polymers60,1164
Non-polymers3,14614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area12170 Å2
ΔGint-205 kcal/mol
Surface area22450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.449, 122.303, 111.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

21A-355-

HOH

31B-314-

HOH

41B-326-

HOH

51B-362-

HOH

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Components

#1: Protein Globin / / Group 2 truncated hemoglobin yjbI / Protozoan/cyanobacterial globin family protein


Mass: 15029.015 Da / Num. of mol.: 2 / Mutation: Y26A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: yjbI, GBAA_1209, BASH2_04647, BVB96_06425 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81TQ7, UniProt: A0A6L7H965*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.5 M Ammonium sulphate / PH range: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 3, 2011 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.14→45.844 Å / Num. obs: 17139 / % possible obs: 90.3 % / Redundancy: 2.15 % / Rmerge(I) obs: 0.072 / Χ2: 0.97 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsΧ2Diffraction-ID% possible all
2.15-2.232.090.312.10.54192.6
2.23-2.322.110.2672.60.64192.4
2.32-2.422.110.2392.70.62192.4
2.42-2.552.10.2093.40.73191.8
2.55-2.712.140.1933.90.73190.4
2.71-2.922.180.1565.10.87189.5
2.92-3.212.150.1296.90.96190.5
3.21-3.682.170.10310.11.17191
3.68-4.632.20.0815.91.47190
4.63-45.812.240.058251.83183.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
d*TREKdata scaling
d*TREK9.9.8.9 W9RSSIdata reduction
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.14→45.844 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 1712 10 %
Rwork0.2114 15405 -
obs0.2135 17117 89.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.55 Å2 / Biso mean: 49.6398 Å2 / Biso min: 26.93 Å2
Refinement stepCycle: final / Resolution: 2.14→45.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 105 135 2263
Biso mean--49.83 49.64 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092197
X-RAY DIFFRACTIONf_angle_d1.0073012
X-RAY DIFFRACTIONf_chiral_restr0.045304
X-RAY DIFFRACTIONf_plane_restr0.007385
X-RAY DIFFRACTIONf_dihedral_angle_d15.761267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1398-2.20270.3181350.27581209134486
2.2027-2.27380.26371450.2661306145191
2.2738-2.35510.28581440.27041302144692
2.3551-2.44940.31311420.24751283142592
2.4494-2.56080.30291430.24361281142492
2.5608-2.69580.25081420.24691280142290
2.6958-2.86470.23541430.24551285142890
2.8647-3.08590.30791430.24541290143390
3.0859-3.39630.26481430.21111280142390
3.3963-3.88750.1881460.18081325147192
3.8875-4.8970.16091440.16461298144289
4.897-45.85440.20081420.18551266140883

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