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- PDB-5v3u: Crystal Structure of the Group II Truncated Hemoglobin from Bacil... -

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Basic information

Entry
Database: PDB / ID: 5v3u
TitleCrystal Structure of the Group II Truncated Hemoglobin from Bacillus Anthracis: Trp90Leu 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: 2.5 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 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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.pdbx_value_order / _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

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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)31,6699
Polymers30,0962
Non-polymers1,5737
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-91 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.216, 122.162, 112.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 15048.060 Da / Num. of mol.: 2 / Mutation: W90L
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


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


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


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
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: Jun 25, 2012
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→42.95 Å / Num. obs: 12420 / % possible obs: 99.9 % / Redundancy: 7.15 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.24 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
d*TREKdata scaling
d*TREK9.9.9.1LDzdata reduction
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→42.95 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 1236 9.98 %
Rwork0.189 --
obs0.193 12380 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 105 80 2215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012202
X-RAY DIFFRACTIONf_angle_d1.013009
X-RAY DIFFRACTIONf_dihedral_angle_d16.7691276
X-RAY DIFFRACTIONf_chiral_restr0.044307
X-RAY DIFFRACTIONf_plane_restr0.006386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60010.3251330.28931213X-RAY DIFFRACTION100
2.6001-2.71840.31961350.2611213X-RAY DIFFRACTION100
2.7184-2.86170.29431370.23321238X-RAY DIFFRACTION100
2.8617-3.04090.28151350.2361224X-RAY DIFFRACTION100
3.0409-3.27570.30631370.22661219X-RAY DIFFRACTION100
3.2757-3.60520.2481360.20481233X-RAY DIFFRACTION100
3.6052-4.12650.1891380.1641235X-RAY DIFFRACTION99
4.1265-5.19750.19351380.14931250X-RAY DIFFRACTION100
5.1975-42.96080.18081470.17171319X-RAY DIFFRACTION100

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