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- PDB-8tls: Crystal structure of Shewanella benthica Group 1 truncated hemogl... -

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Basic information

Entry
Database: PDB / ID: 8tls
TitleCrystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S Y108A variant
ComponentsGroup 1 truncated hemoglobin
KeywordsHEME BINDING PROTEIN / GLOBIN / 2/2 HEMOGLOBIN / UNKNOWN FUNCTION / PSYCHROPIEZOPHILE
Function / homology
Function and homology information


oxygen transport / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin, bacterial-like, conserved site / Protozoan/cyanobacterial globins signature. / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globin-like superfamily
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Group 1 truncated hemoglobin
Similarity search - Component
Biological speciesShewanella benthica KT99 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 Å
AuthorsSchultz, T.D. / Martinez, J.E. / Siegler, M.A. / Schlessman, J.L. / Lecomte, J.T.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1330488 United States
National Science Foundation (NSF, United States)CHE-2003950 United States
National Science Foundation (NSF, United States)GRFP-1746891 United States
CitationJournal: To Be Published
Title: Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S Y108A variant
Authors: Schultz, T.D. / Martinez, J.E. / Siegler, M.A. / Schlessman, J.L. / Lecomte, J.T.J.
History
DepositionJul 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Group 1 truncated hemoglobin
B: Group 1 truncated hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7786
Polymers25,4932
Non-polymers1,2854
Water5,531307
1
A: Group 1 truncated hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3893
Polymers12,7461
Non-polymers6432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Group 1 truncated hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3893
Polymers12,7461
Non-polymers6432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.718, 66.718, 125.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

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Components

#1: Protein Group 1 truncated hemoglobin


Mass: 12746.330 Da / Num. of mol.: 2 / Mutation: C51S, C71S, Y108A
Source method: isolated from a genetically manipulated source
Details: First residue of reference sequence A9DF82 (Met) is cleaved by E. coli; first residue of sample (Ser) is numbered 2.
Source: (gene. exp.) Shewanella benthica KT99 (bacteria) / Strain: KT99 / Gene: KT99_16901 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9DF82
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CN
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 27% PEG MME 2000, 100 mM Bis-Tris pH 5.1, 10 mM KCN, Excluded from light
PH range: 5.1-6.0 / Temp details: Room Temp

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 29, 2022 / Details: NULL
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→24.28 Å / Num. obs: 59860 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.063 / Net I/σ(I): 24.07
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.08 / Num. unique obs: 5978 / Rsym value: 0.221 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(dev_4788: ???)refinement
CrysalisPro1.171.42.49data scaling
PHENIXdev-4788-000phasing
CrysalisPro1.171.42.49data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→21.9 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 20.83 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2139 1995 6.27 %
Rwork0.1891 --
obs0.1907 31799 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 90 307 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082004
X-RAY DIFFRACTIONf_angle_d1.0742739
X-RAY DIFFRACTIONf_dihedral_angle_d9.767320
X-RAY DIFFRACTIONf_chiral_restr0.053288
X-RAY DIFFRACTIONf_plane_restr0.008351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.28221400.21192085X-RAY DIFFRACTION100
1.74-1.790.20761400.18812085X-RAY DIFFRACTION100
1.79-1.840.24741420.19392110X-RAY DIFFRACTION100
1.84-1.90.25161380.2292084X-RAY DIFFRACTION100
1.9-1.970.26521410.22642106X-RAY DIFFRACTION100
1.97-2.050.23211400.19582090X-RAY DIFFRACTION100
2.05-2.140.21571410.18092111X-RAY DIFFRACTION100
2.14-2.250.2361420.20082105X-RAY DIFFRACTION100
2.25-2.40.20241420.19422119X-RAY DIFFRACTION100
2.4-2.580.18781420.17592125X-RAY DIFFRACTION100
2.58-2.840.17971440.17842142X-RAY DIFFRACTION100
2.84-3.250.1951440.18362159X-RAY DIFFRACTION100
3.25-4.090.18971460.17442163X-RAY DIFFRACTION98
4.09-21.90.21381530.17472320X-RAY DIFFRACTION99

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