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- PDB-6j1f: Crystal structure of HypX from Aquifex aeolicus in complex with T... -

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Basic information

Entry
Database: PDB / ID: 6j1f
TitleCrystal structure of HypX from Aquifex aeolicus in complex with Tetrahydrofolic acid
Components(Hydrogenase regulation ...) x 2
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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
COENZYME A / (6S)-5,6,7,8-TETRAHYDROFOLATE / Hydrogenase regulation HoxX
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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Assembly

Deposited unit
A: Hydrogenase regulation HoxX
B: Hydrogenase regulation HoxX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,9517
Polymers134,7862
Non-polymers2,1655
Water3,531196
1
A: Hydrogenase regulation HoxX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0724
Polymers67,7661
Non-polymers1,3053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area24240 Å2
MethodPISA
2
B: Hydrogenase regulation HoxX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8793
Polymers67,0201
Non-polymers8602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.020, 123.735, 290.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Hydrogenase regulation ... , 2 types, 2 molecules AB

#1: Protein Hydrogenase regulation HoxX


Mass: 67766.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: hoxX, aq_1156 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O67224
#2: Protein Hydrogenase regulation HoxX


Mass: 67019.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: hoxX, aq_1156 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O67224

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Non-polymers , 4 types, 201 molecules

#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


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


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


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, HEPES-NaOH, Glycerol / 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: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 84116 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 45.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 15.24
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 8275 / CC1/2: 0.713 / Rpim(I) all: 0.36 / Rrim(I) all: 0.934 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J0P

6j0p


Resolution: 2.1→42.314 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 4205 5 %Random selection
Rwork0.1774 ---
obs0.1792 84107 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9045 0 140 196 9381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089444
X-RAY DIFFRACTIONf_angle_d0.85212792
X-RAY DIFFRACTIONf_dihedral_angle_d16.1995601
X-RAY DIFFRACTIONf_chiral_restr0.0521339
X-RAY DIFFRACTIONf_plane_restr0.0051641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.2971330.26572559X-RAY DIFFRACTION99
2.1239-2.14890.28371460.23852657X-RAY DIFFRACTION100
2.1489-2.17510.26181340.22392647X-RAY DIFFRACTION100
2.1751-2.20260.26041360.21352603X-RAY DIFFRACTION100
2.2026-2.23160.26971410.20882693X-RAY DIFFRACTION100
2.2316-2.26220.27281360.20292591X-RAY DIFFRACTION100
2.2622-2.29450.23671430.20292688X-RAY DIFFRACTION100
2.2945-2.32870.25691400.18982603X-RAY DIFFRACTION100
2.3287-2.36510.24481370.19142659X-RAY DIFFRACTION100
2.3651-2.40390.22741440.18642627X-RAY DIFFRACTION100
2.4039-2.44530.24961370.18752646X-RAY DIFFRACTION100
2.4453-2.48980.24081390.1952639X-RAY DIFFRACTION100
2.4898-2.53770.26161380.18682679X-RAY DIFFRACTION100
2.5377-2.58950.23661400.19352618X-RAY DIFFRACTION100
2.5895-2.64570.26481410.19192677X-RAY DIFFRACTION100
2.6457-2.70730.22321360.19012641X-RAY DIFFRACTION100
2.7073-2.7750.24071380.19322631X-RAY DIFFRACTION100
2.775-2.850.22721460.19772681X-RAY DIFFRACTION100
2.85-2.93380.24681350.20092678X-RAY DIFFRACTION100
2.9338-3.02850.23481420.20152604X-RAY DIFFRACTION100
3.0285-3.13670.26341390.2022683X-RAY DIFFRACTION100
3.1367-3.26230.2421410.19532673X-RAY DIFFRACTION100
3.2623-3.41070.20531400.18352660X-RAY DIFFRACTION100
3.4107-3.59040.21951400.17672674X-RAY DIFFRACTION100
3.5904-3.81520.20541450.16692699X-RAY DIFFRACTION100
3.8152-4.10960.19571380.15762708X-RAY DIFFRACTION100
4.1096-4.52270.14331440.13912687X-RAY DIFFRACTION100
4.5227-5.17610.17341420.14772723X-RAY DIFFRACTION100
5.1761-6.51760.22461450.17672728X-RAY DIFFRACTION100
6.5176-42.3140.19041490.17462846X-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)
11.4155-0.0512-0.08871.10610.06920.8173-0.06550.10910.0455-0.09470.03780.0146-0.0906-0.00250.02860.3197-0.0132-0.01750.3158-0.03830.3387-14.8129-18.569120.5751
22.14950.2704-0.12462.69150.35871.05270.0445-0.5378-0.09230.612-0.206-0.068-0.00380.05680.13150.4826-0.0624-0.05820.52960.06240.32321.4232-11.018256.3385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid -1 through 562)
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 556)

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