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- PDB-3s1j: Crystal structure of acetate-bound hell's gate globin I -

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Basic information

Entry
Database: PDB / ID: 3s1j
TitleCrystal structure of acetate-bound hell's gate globin I
ComponentsHemoglobin-like flavoprotein
KeywordsOXYGEN TRANSPORT / OXYGEN STORAGE / GLOBIN / HEME / ACETATE-BOUND / AUTOXIDATION
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / response to hypoxia / 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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin-like flavoprotein
Similarity search - Component
Biological speciesMethylacidiphilum infernorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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)50,09412
Polymers47,7793
Non-polymers2,3159
Water4,648258
1
A: Hemoglobin-like flavoprotein
B: Hemoglobin-like flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3968
Polymers31,8522
Non-polymers1,5436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-78 kcal/mol
Surface area13210 Å2
MethodPISA
2
C: Hemoglobin-like flavoprotein
hetero molecules

C: Hemoglobin-like flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3968
Polymers31,8522
Non-polymers1,5436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4850 Å2
ΔGint-78 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.034, 126.225, 148.395
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-236-

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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 258 / 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: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.0M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Oct 16, 2009
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→38.93 Å / Num. obs: 59437 / % possible obs: 97.2 % / Redundancy: 2.93 % / Biso Wilson estimate: 32.95 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.01 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.8 / % possible all: 88.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX1.7.1_743refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.48 Å / SU ML: 0.58 / σ(F): 1.34 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 1961 3.3 %
Rwork0.2092 --
obs0.2101 59417 97.15 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.064 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 32.6131 Å2
Baniso -1Baniso -2Baniso -3
1--1.9703 Å2-0 Å20 Å2
2---1.7226 Å20 Å2
3---3.693 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 156 258 3546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083436
X-RAY DIFFRACTIONf_angle_d0.9894699
X-RAY DIFFRACTIONf_dihedral_angle_d15.6221286
X-RAY DIFFRACTIONf_chiral_restr0.068495
X-RAY DIFFRACTIONf_plane_restr0.004591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.40431230.39633646X-RAY DIFFRACTION87
1.845-1.89490.35921420.35013844X-RAY DIFFRACTION93
1.8949-1.95070.30051440.30024184X-RAY DIFFRACTION100
1.9507-2.01360.25581400.26524155X-RAY DIFFRACTION100
2.0136-2.08560.28421360.23814176X-RAY DIFFRACTION100
2.0856-2.16910.23731490.21994195X-RAY DIFFRACTION100
2.1691-2.26780.23781410.21844222X-RAY DIFFRACTION100
2.2678-2.38730.24741440.2124166X-RAY DIFFRACTION100
2.3873-2.53690.2921420.22444183X-RAY DIFFRACTION99
2.5369-2.73270.24691460.21014193X-RAY DIFFRACTION99
2.7327-3.00760.21151480.21324199X-RAY DIFFRACTION99
3.0076-3.44260.22451450.20134144X-RAY DIFFRACTION98
3.4426-4.33630.20781310.17514039X-RAY DIFFRACTION94
4.3363-38.48890.21881300.1924110X-RAY DIFFRACTION92

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