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- PDB-8vgu: Crystal structure of BcTSPO/Hematin complex -

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Basic information

Entry
Database: PDB / ID: 8vgu
TitleCrystal structure of BcTSPO/Hematin complex
ComponentsTryptophan-rich protein TspO
KeywordsMEMBRANE PROTEIN / TSPO / Oxygenase / Porphyrin / Bilindigin
Function / homologyMesoheme / Chem-MPG / OXYGEN MOLECULE / :
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsQiu, W. / Guo, Y. / Hendrickson, W.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107462 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116799 United States
CitationJournal: PNAS
Title: Crystal structure of BcTSPO complexed with hematin
Authors: Qiu, W. / Guo, Y. / Hendrickson, W.A.
History
DepositionDec 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan-rich protein TspO
B: Tryptophan-rich protein TspO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,15114
Polymers42,9942
Non-polymers4,15712
Water1,04558
1
A: Tryptophan-rich protein TspO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2196
Polymers21,4971
Non-polymers1,7225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan-rich protein TspO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9328
Polymers21,4971
Non-polymers2,4357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.523, 46.983, 67.853
Angle α, β, γ (deg.)90.00, 92.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tryptophan-rich protein TspO


Mass: 21496.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BW896_26980 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9Q5MS21
#2: Chemical ChemComp-MH0 / Mesoheme


Mass: 620.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6
Details: 0.1 M sodium chloride, 0.02 M Sodium citrate, pH5.6, 5.5% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Mar 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 22098 / % possible obs: 99.2 % / Redundancy: 1.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Net I/σ(I): 42.6
Reflection shellResolution: 2.03→2.27 Å / Rmerge(I) obs: 0.499 / Num. unique obs: 3444

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RYO

4ryo


Resolution: 2.03→29.162 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1028 4.7 %
Rwork0.2179 --
obs0.2196 21871 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→29.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 187 58 2705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042748
X-RAY DIFFRACTIONf_angle_d0.8153750
X-RAY DIFFRACTIONf_dihedral_angle_d14.743907
X-RAY DIFFRACTIONf_chiral_restr0.027401
X-RAY DIFFRACTIONf_plane_restr0.003424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.1370.31831700.27512949X-RAY DIFFRACTION100
2.137-2.27090.3241330.22072946X-RAY DIFFRACTION99
2.2709-2.44610.27231410.21552980X-RAY DIFFRACTION99
2.4461-2.69210.26161490.20222973X-RAY DIFFRACTION100
2.6921-3.08130.24231290.20112989X-RAY DIFFRACTION99
3.0813-3.88070.22621440.21912984X-RAY DIFFRACTION99
3.8807-50.24341620.21853022X-RAY DIFFRACTION99

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