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- PDB-7dih: Crystal structure of Thermoglobin Y29F mutant in complex with imi... -

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Basic information

Entry
Database: PDB / ID: 7dih
TitleCrystal structure of Thermoglobin Y29F mutant in complex with imidazole
ComponentsThermoglobin
KeywordsOXYGEN BINDING / hemoglobin / monomer
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Uncharacterized globin-like protein aq_211
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMuraki, N. / Aono, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H05762 Japan
CitationJournal: Chem Lett. / Year: 2021
Title: Structural Characterization of Y29F Mutant of Thermoglobin from a Hyperthermophilic Bacterium Aquifex aeolicus
Authors: Muraki, N. / Takeda, K. / Nam, D. / Muraki, M. / Aono, S.
History
DepositionNov 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermoglobin
B: Thermoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9737
Polymers32,5052
Non-polymers1,4675
Water1,33374
1
A: Thermoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0344
Polymers16,2531
Non-polymers7823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-21 kcal/mol
Surface area7610 Å2
MethodPISA
2
B: Thermoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9383
Polymers16,2531
Non-polymers6862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-21 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.771, 35.823, 138.084
Angle α, β, γ (deg.)90.00, 95.20, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Thermoglobin


Mass: 16252.726 Da / Num. of mol.: 2 / Mutation: Y29F
Source method: isolated from a genetically manipulated source
Details: N-terminal three amino acids (GSH) is a part of expression tag, which was digested by protease.
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: aq_211 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O66586
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.69 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 3.0 M ammonium sulfide, 0.1 M sodium cacodylate pH 6.0, 2 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→38.03 Å / Num. obs: 46830 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.024 / Rrim(I) all: 0.046 / Net I/σ(I): 18.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2116 / Rpim(I) all: 0.501 / Rrim(I) all: 0.807 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata processing
BUCCANEERmodel building
MOLREPphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vhb

1vhb


Resolution: 1.5→38.022 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 4417 4.87 %Random selection
Rwork0.1993 ---
obs0.2004 46816 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→38.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 101 74 2352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072387
X-RAY DIFFRACTIONf_angle_d0.8293276
X-RAY DIFFRACTIONf_dihedral_angle_d17.0711444
X-RAY DIFFRACTIONf_chiral_restr0.042369
X-RAY DIFFRACTIONf_plane_restr0.005402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.33051100.30222610X-RAY DIFFRACTION92
1.5171-1.53490.27681310.29892799X-RAY DIFFRACTION95
1.5349-1.55360.27911530.28722883X-RAY DIFFRACTION98
1.5536-1.57330.29721690.25762816X-RAY DIFFRACTION100
1.5733-1.5940.24171280.24542909X-RAY DIFFRACTION100
1.594-1.61580.25571810.23022906X-RAY DIFFRACTION100
1.6158-1.63890.25811540.22272837X-RAY DIFFRACTION100
1.6389-1.66340.23381370.21342951X-RAY DIFFRACTION100
1.6634-1.68940.20671340.20852885X-RAY DIFFRACTION100
1.6894-1.71710.26531420.19482861X-RAY DIFFRACTION100
1.7171-1.74670.21811620.20292940X-RAY DIFFRACTION100
1.7467-1.77840.21791500.19922871X-RAY DIFFRACTION100
1.7784-1.81260.2061290.19882879X-RAY DIFFRACTION99
1.8126-1.84960.24151630.20022867X-RAY DIFFRACTION100
1.8496-1.88990.23271620.19692956X-RAY DIFFRACTION100
1.8899-1.93380.20631680.18642812X-RAY DIFFRACTION100
1.9338-1.98220.21031540.19142939X-RAY DIFFRACTION100
1.9822-2.03580.25841190.19732836X-RAY DIFFRACTION99
2.0358-2.09570.18491550.18622961X-RAY DIFFRACTION100
2.0957-2.16330.17751450.17762838X-RAY DIFFRACTION100
2.1633-2.24060.23291340.18512920X-RAY DIFFRACTION100
2.2406-2.33030.21161520.18472871X-RAY DIFFRACTION100
2.3303-2.43630.2341490.18552870X-RAY DIFFRACTION100
2.4363-2.56480.19881700.18972921X-RAY DIFFRACTION100
2.5648-2.72540.19841330.19212886X-RAY DIFFRACTION100
2.7254-2.93580.22861590.21382885X-RAY DIFFRACTION100
2.9358-3.23110.25731570.22112907X-RAY DIFFRACTION100
3.2311-3.69830.22271440.20172879X-RAY DIFFRACTION100
3.6983-4.65810.19871420.17492913X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7611-0.2456-0.32361.28780.1372.7931-0.03970.0901-0.032-0.07820.04240.01530.067-0.2481-0.0130.1508-0.0111-0.00410.15740.020.174419.7844-18.378319.798
22.5509-0.07221.16991.3366-0.10082.8820.0136-0.0932-0.19840.05240.04310.12690.1095-0.1586-0.0550.1940.00710.00660.14930.00160.214313.8511-20.2375-18.2013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 137)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 137)

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