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- PDB-6j1h: Crystal structure of HypX from Aquifex aeolicus, Q15A-R131A-S194A... -

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Basic information

Entry
Database: PDB / ID: 6j1h
TitleCrystal structure of HypX from Aquifex aeolicus, Q15A-R131A-S194A-Q195A-N306A-R542A variant
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
Hydrogenase regulation HoxX
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 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)135,0264
Polymers134,8422
Non-polymers1842
Water1,36976
1
A: Hydrogenase regulation HoxX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5132
Polymers67,4211
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area24450 Å2
MethodPISA
2
B: Hydrogenase regulation HoxX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5132
Polymers67,4211
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.915, 124.409, 290.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hydrogenase regulation HoxX


Mass: 67421.086 Da / Num. of mol.: 2 / Mutation: Q15A, R131A, S194A, Q195A,N306A, R542A
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs.
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 12% PEG3350, HEPES-NaOH, 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: Jul 21, 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: 84408 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 44.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Net I/σ(I): 17.09
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.84 / Num. unique obs: 8263 / CC1/2: 0.936 / Rpim(I) all: 0.35 / Rrim(I) all: 0.91 / % possible all: 98.5

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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: 2.101→47.248 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 3845 2.37 %Random selection
Rwork0.2002 ---
obs0.2011 84393 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.101→47.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9090 0 12 76 9178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079398
X-RAY DIFFRACTIONf_angle_d0.79612706
X-RAY DIFFRACTIONf_dihedral_angle_d13.2635638
X-RAY DIFFRACTIONf_chiral_restr0.0521339
X-RAY DIFFRACTIONf_plane_restr0.0051636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1007-2.12730.36151350.34695429X-RAY DIFFRACTION93
2.1273-2.15530.33271430.32045954X-RAY DIFFRACTION100
2.1553-2.18480.35281400.30795901X-RAY DIFFRACTION100
2.1848-2.2160.34771450.29285895X-RAY DIFFRACTION100
2.216-2.24910.39451420.28155879X-RAY DIFFRACTION100
2.2491-2.28420.26391430.26545903X-RAY DIFFRACTION100
2.2842-2.32170.29011410.25035828X-RAY DIFFRACTION99
2.3217-2.36170.26021470.23335901X-RAY DIFFRACTION100
2.3617-2.40460.22531420.22445893X-RAY DIFFRACTION100
2.4046-2.45090.26521410.22345918X-RAY DIFFRACTION100
2.4509-2.50090.22931430.22815876X-RAY DIFFRACTION100
2.5009-2.55530.27451430.22045924X-RAY DIFFRACTION100
2.5553-2.61470.26061410.22075859X-RAY DIFFRACTION100
2.6147-2.68010.29241440.23165898X-RAY DIFFRACTION100
2.6801-2.75260.29121460.22595941X-RAY DIFFRACTION100
2.7526-2.83350.29941410.22955913X-RAY DIFFRACTION100
2.8335-2.9250.27441420.23095807X-RAY DIFFRACTION100
2.925-3.02950.24171420.22725899X-RAY DIFFRACTION100
3.0295-3.15080.26431460.23125826X-RAY DIFFRACTION99
3.1508-3.29410.3021410.23465865X-RAY DIFFRACTION99
3.2941-3.46780.25571440.215842X-RAY DIFFRACTION99
3.4678-3.6850.21671420.19545897X-RAY DIFFRACTION100
3.685-3.96930.21531440.17675836X-RAY DIFFRACTION100
3.9693-4.36850.18221380.15765893X-RAY DIFFRACTION99
4.3685-5.00010.18731420.1465873X-RAY DIFFRACTION99
5.0001-6.29720.20561460.17755768X-RAY DIFFRACTION98
6.2972-47.25990.19141410.16935843X-RAY DIFFRACTION99
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)
11.01020.0067-0.2060.91090.09090.6607-0.03590.149-0.0219-0.09730.01560.0252-0.0446-0.04750.01980.2983-0.0151-0.00820.3269-0.03820.2782-14.8559-18.716920.7431
21.83930.2582-0.08992.3867-0.04650.85160.0462-0.4790.02770.5552-0.1507-0.0313-0.05770.05260.09630.4264-0.0261-0.00610.49610.00430.286721.0574-11.209556.8149
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 -1 through 561)

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