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- PDB-4nk2: Crystal structure of Hell's gate globin IV -

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Basic information

Entry
Database: PDB / ID: 4nk2
TitleCrystal structure of Hell's gate globin IV
ComponentsHemoglobin-like protein
KeywordsOXYGEN BINDING / Truncated / Hemoglobins / Heme / Truncated hemoglobin
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Two-on-two hemoglobin-3 / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin-like protein
Similarity search - Component
Biological speciesMethylacidiphilum infernorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsJamil, F.
CitationJournal: J.Biochem. / Year: 2014
Title: Crystal structure of truncated haemoglobin from an extremely thermophilic and acidophilic bacterium.
Authors: Jamil, F. / Teh, A.H. / Schadich, E. / Saito, J.A. / Najimudin, N. / Alam, M.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin-like protein
B: Hemoglobin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6404
Polymers45,4072
Non-polymers1,2332
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-53 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.217, 83.427, 94.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit consist of two identical subuints.

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Components

#1: Protein Hemoglobin-like protein


Mass: 22703.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylacidiphilum infernorum (bacteria)
Strain: V4 / Gene: Minf_1222 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS / References: UniProt: B3DVC3
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% (v/v) 2-methyl-2,4-pentanediol in 0.05 M citric acid pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Apr 27, 2012
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→38.71 Å / Num. all: 38333 / Num. obs: 38333 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.44 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.3
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 2.32 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2 / Num. unique all: 3688 / % possible all: 95.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NK1

4nk1


Resolution: 1.96→35.114 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1907 4.98 %RANDOM
Rwork0.2096 ---
obs0.2116 38302 97.74 %-
all-38302 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.083 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.1278 Å20 Å20 Å2
2--7.5182 Å20 Å2
3---3.6096 Å2
Refinement stepCycle: LAST / Resolution: 1.96→35.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 86 235 3049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082943
X-RAY DIFFRACTIONf_angle_d1.0514010
X-RAY DIFFRACTIONf_dihedral_angle_d15.5811090
X-RAY DIFFRACTIONf_chiral_restr0.069404
X-RAY DIFFRACTIONf_plane_restr0.004502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0090.39371330.34472481X-RAY DIFFRACTION96
2.009-2.06330.33141340.32732510X-RAY DIFFRACTION96
2.0633-2.12410.4021340.29562553X-RAY DIFFRACTION97
2.1241-2.19260.30731340.27472552X-RAY DIFFRACTION97
2.1926-2.2710.28411330.25082541X-RAY DIFFRACTION97
2.271-2.36190.29841320.25112599X-RAY DIFFRACTION98
2.3619-2.46930.27971390.23762605X-RAY DIFFRACTION99
2.4693-2.59950.27761380.23012630X-RAY DIFFRACTION100
2.5995-2.76230.30781390.22592642X-RAY DIFFRACTION100
2.7623-2.97550.24471390.19582654X-RAY DIFFRACTION100
2.9755-3.27470.21041390.19992662X-RAY DIFFRACTION100
3.2747-3.74810.26061410.18382673X-RAY DIFFRACTION99
3.7481-4.72040.22351400.17152653X-RAY DIFFRACTION98
4.7204-35.11980.21181320.21192640X-RAY DIFFRACTION93

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