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- PDB-6j1e: Crystal structure of HypX from Aquifex aeolicus (Crystal Form II) -

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Basic information

Entry
Database: PDB / ID: 6j1e
TitleCrystal structure of HypX from Aquifex aeolicus (Crystal Form II)
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 / Hydrogenase regulation HoxX
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)68,5342
Polymers67,7661
Non-polymers7681
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-2 kcal/mol
Surface area23530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.320, 88.320, 162.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hydrogenase regulation HoxX / HypX


Mass: 67766.445 Da / Num. of mol.: 1
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 / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, HEPES-NaOH / PH range: 7.0-7.5

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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: RAYONIX MX300HE / Detector: CCD / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25797 / % possible obs: 99.4 % / Redundancy: 14.5 % / Biso Wilson estimate: 49.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.026 / Rrim(I) all: 0.1 / Net I/σ(I): 19.47
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 4.26 / Num. unique obs: 2502 / CC1/2: 0.929 / Rpim(I) all: 0.179 / Rrim(I) all: 0.694 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→44.16 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 1292 5 %Random selection
Rwork0.1832 ---
obs-25789 99.4 %-
Displacement parametersBiso mean: 55.86 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4455 0 48 2 4505
LS refinement shellResolution: 2.4→2.496 Å
RfactorNum. reflection% reflection
Rfree0.3543 143 -
Rwork0.2438 2634 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: 53.0715 Å / Origin y: 6.3112 Å / Origin z: 67.5324 Å
111213212223313233
T0.3649 Å20.0477 Å20.0511 Å2-0.2968 Å20.056 Å2--0.282 Å2
L1.249 °2-0.058 °2-0.0072 °2-1.6103 °20.4846 °2--1.3693 °2
S0.1416 Å °0.0962 Å °0.1056 Å °-0.1825 Å °-0.134 Å °-0.0195 Å °-0.3026 Å °-0.129 Å °-0.0022 Å °
Refinement TLS groupSelection details: all

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