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- PDB-6j1j: Crystal structure of HypX from Aquifex aeolicus, A392F-I419F vari... -

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Basic information

Entry
Database: PDB / ID: 6j1j
TitleCrystal structure of HypX from Aquifex aeolicus, A392F-I419F variant in complex with Tetrahydrofolic acid
ComponentsHydrogenase regulation HoxX
KeywordsBIOSYNTHETIC PROTEIN / Hydrogenase / maturation / carbon monoxide
Function / homology
Function and homology information


biosynthetic process / catalytic activity
Similarity search - Function
[NiFe]-hydrogenase maturation factor, HypX/HoxX type / : / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. ...[NiFe]-hydrogenase maturation factor, HypX/HoxX type / : / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
COENZYME A / (6S)-5,6,7,8-TETRAHYDROFOLATE / Hydrogenase regulation HoxX
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMuraki, N. / Aono, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17H03093 Japan
CitationJournal: Commun Biol / Year: 2019
Title: Structural characterization of HypX responsible for CO biosynthesis in the maturation of NiFe-hydrogenase.
Authors: Muraki, N. / Ishii, K. / Uchiyama, S. / Itoh, S.G. / Okumura, H. / Aono, S.
History
DepositionDec 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrogenase regulation HoxX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2745
Polymers67,8771
Non-polymers1,3974
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-1 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.429, 141.891, 170.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-706-

HOH

21A-741-

HOH

31A-770-

HOH

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Components

#1: Protein Hydrogenase regulation HoxX


Mass: 67876.547 Da / Num. of mol.: 1 / Mutation: A392F, I419F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: hoxX, aq_1156 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O67224
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 16% PEG4000, 20% 2-propanol, 8% glycerol

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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: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 57352 / % possible obs: 99.9 % / Redundancy: 51.5 % / Biso Wilson estimate: 41.53 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.034 / Rrim(I) all: 0.179 / Net I/σ(I): 14.97
Reflection shellResolution: 2→2.05 Å / Redundancy: 39.2 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5640 / CC1/2: 0.966 / Rpim(I) all: 0.284 / Rrim(I) all: 1.29 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J0P

6j0p


Resolution: 2→39.09 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 2000 -Random selection
Rwork0.1797 ---
obs-57317 99.9 %-
Displacement parametersBiso mean: 41.53 Å2
Refinement stepCycle: LAST / Resolution: 2→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4571 0 92 80 4743
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.2855 197 -
Rwork0.2338 5639 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: -13.6026 Å / Origin y: -26.3597 Å / Origin z: -22.9863 Å
111213212223313233
T0.3121 Å20.0022 Å20.0152 Å2-0.3032 Å2-0.0651 Å2--0.2672 Å2
L2.0704 °20.6501 °2-0.0799 °2-1.2308 °20.01 °2--1.0884 °2
S0.1214 Å °-0.2916 Å °0.1692 Å °0.0897 Å °-0.0578 Å °0.123 Å °0.0663 Å °0.0441 Å °-0.0629 Å °
Refinement TLS groupSelection details: ALL

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