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- PDB-3s1i: Crystal structure of oxygen-bound hell's gate globin I -

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Basic information

Entry
Database: PDB / ID: 3s1i
TitleCrystal structure of oxygen-bound hell's gate globin I
ComponentsHemoglobin-like flavoprotein
KeywordsOXYGEN TRANSPORT / OXYGEN STORAGE / GLOBIN / HEME / OXYGEN-BOUND / AUTOXIDATION
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin-like flavoprotein
Similarity search - Component
Biological speciesMethylacidiphilum infernorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsTeh, A.H. / Saito, J.A. / Baharuddin, A. / Tuckerman, J.R. / Newhouse, J.S. / Kanbe, M. / Newhouse, E.I. / Rahim, R.A. / Favier, F. / Didierjean, C. ...Teh, A.H. / Saito, J.A. / Baharuddin, A. / Tuckerman, J.R. / Newhouse, J.S. / Kanbe, M. / Newhouse, E.I. / Rahim, R.A. / Favier, F. / Didierjean, C. / Sousa, E.H.S. / Stott, M.B. / Dunfield, P.F. / Gonzalez, G. / Gilles-Gonzalez, M.A. / Najimudin, N. / Alam, M.
CitationJournal: Febs Lett. / Year: 2011
Title: Hell's Gate globin I: an acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin
Authors: Teh, A.H. / Saito, J.A. / Baharuddin, A. / Tuckerman, J.R. / Newhouse, J.S. / Kanbe, M. / Newhouse, E.I. / Rahim, R.A. / Favier, F. / Didierjean, C. / Sousa, E.H.S. / Stott, M.B. / Dunfield, ...Authors: Teh, A.H. / Saito, J.A. / Baharuddin, A. / Tuckerman, J.R. / Newhouse, J.S. / Kanbe, M. / Newhouse, E.I. / Rahim, R.A. / Favier, F. / Didierjean, C. / Sousa, E.H.S. / Stott, M.B. / Dunfield, P.F. / Gonzalez, G. / Gilles-Gonzalez, M.A. / Najimudin, N. / Alam, M.
History
DepositionMay 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin-like flavoprotein
B: Hemoglobin-like flavoprotein
C: Hemoglobin-like flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,01212
Polymers47,7793
Non-polymers2,2349
Water3,333185
1
A: Hemoglobin-like flavoprotein
B: Hemoglobin-like flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3428
Polymers31,8522
Non-polymers1,4896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-76 kcal/mol
Surface area13270 Å2
MethodPISA
2
C: Hemoglobin-like flavoprotein
hetero molecules

C: Hemoglobin-like flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3428
Polymers31,8522
Non-polymers1,4896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4550 Å2
ΔGint-77 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.092, 126.181, 147.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-163-

HOH

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Components

#1: Protein Hemoglobin-like flavoprotein / Hell'S Gate Globin I


Mass: 15926.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylacidiphilum infernorum (bacteria)
Strain: V4 / Gene: hmp, Minf_1095 / Plasmid: PET-3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2(DE3)PLYSS / References: UniProt: B3DUZ7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#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.: 185 / 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: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 298 K / pH: 8
Details: Obtained by transferring acetate-bound crystals (3S1J) to 1.8M ammonium sulphate, 0.1M Tris-HCl, pH 8.0, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 19, 2010
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→36.07 Å / Num. obs: 63721 / % possible obs: 99.9 % / Redundancy: 3.88 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.8
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX1.7.1_743refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→35.046 Å / SU ML: 0.54 / σ(F): 1.34 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 1984 3.11 %
Rwork0.2068 --
obs0.2073 63705 99.85 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.916 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8289 Å20 Å20 Å2
2--1.8567 Å20 Å2
3---3.9721 Å2
Refinement stepCycle: LAST / Resolution: 1.77→35.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 150 185 3467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073396
X-RAY DIFFRACTIONf_angle_d0.9774637
X-RAY DIFFRACTIONf_dihedral_angle_d15.0371262
X-RAY DIFFRACTIONf_chiral_restr0.069490
X-RAY DIFFRACTIONf_plane_restr0.005579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.81430.42061300.42764365X-RAY DIFFRACTION100
1.8143-1.86330.40861390.38434394X-RAY DIFFRACTION100
1.8633-1.91820.39031480.33474332X-RAY DIFFRACTION100
1.9182-1.98010.2961360.26914396X-RAY DIFFRACTION100
1.9801-2.05080.24911420.23584366X-RAY DIFFRACTION100
2.0508-2.13290.23571440.21444382X-RAY DIFFRACTION100
2.1329-2.230.26291390.20654379X-RAY DIFFRACTION100
2.23-2.34750.23861460.2074391X-RAY DIFFRACTION100
2.3475-2.49460.21621380.2194410X-RAY DIFFRACTION100
2.4946-2.68710.22451400.20834402X-RAY DIFFRACTION100
2.6871-2.95740.24491440.2144410X-RAY DIFFRACTION100
2.9574-3.38510.19881410.20714445X-RAY DIFFRACTION100
3.3851-4.26360.19461480.17184476X-RAY DIFFRACTION100
4.2636-35.05290.20221490.18824573X-RAY DIFFRACTION99

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