PDB-6j0p: Crystal structure of HypX from Aquifex aeolicus (Crystal Form I)

ID or keywords:

Entry

Database: PDB / ID: 6j0p

Title

Crystal structure of HypX from Aquifex aeolicus (Crystal Form I)

Components

Hydrogenase regulation HoxX

Keywords

BIOSYNTHETIC PROTEIN / Hydrogenase / maturation / carbon monoxide

Function / homology

Function and homology information

biosynthetic process / catalytic activity
Similarity search - Function

Biological species

Aquifex aeolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.79 Å

Authors

Muraki, N. / Aono, S.

Funding support

Japan, 1items

Citation

Journal: 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

Deposition	Dec 25, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6j0p.cif.gz	474.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6j0p.ent.gz	390 KB	Display	PDB format
PDBx/mmJSON format	6j0p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6j0p_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6j0p_full_validation.pdf.gz	1 MB	Display
Data in XML	6j0p_validation.xml.gz	44.1 KB	Display
Data in CIF	6j0p_validation.cif.gz	62.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j0/6j0p ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j0p	HTTPS FTP

-
Related structure data

Related structure data	6j1eC 6j1fC 6j1gC 6j1hC 6j1iC 6j1jC C: citing same article (ref.)
Similar structure data	6j1h-1 4mj2-1 1e6e-1 6j1i-d 6j1f-2 6j1f-1 4mj4-d 2v45-d 4yzz-d 6i6x-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Hydrogenase regulation HoxX

B: Hydrogenase regulation HoxX

hetero molecules

137 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hydrogenase regulation HoxX

hetero molecules

defined by author&software
Evidence: gel filtration
68.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hydrogenase regulation HoxX

hetero molecules

defined by author&software
68.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.840, 124.300, 290.850
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Hydrogenase regulation HoxX / HypX Mass: 67766.445 Da / Num. of mol.: 2 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 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O67224
#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.74 Å³/Da / Density % sol: 55.16 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, HEPES-NaOH / PH range: 7.0 - 7.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 1.79→42.47 Å / Num. obs: 134916 / % possible obs: 98.8 % / Redundancy: 7.5 % / B_iso Wilson estimate: 28.65 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.073 / R_pim(I) all: 0.029 / R_rim(I) all: 0.078 / Net I/σ(I): 16.77
Reflection shell	Resolution: 1.79→1.86 Å / Redundancy: 7.5 % / R_merge(I) obs: 1.094 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11960 / CC_1/2: 0.677 / R_pim(I) all: 0.4255 / R_rim(I) all: 1.175 / % possible all: 89.1

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.79→42.47 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 19.48

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.196	6685	5 %	Random selection
R_work	0.173	-	-	-
obs	0.1739	133690	98.74 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.79→42.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9174	0	108	392	9674

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9666
X-RAY DIFFRACTION	f_angle_d	0.813	13085
X-RAY DIFFRACTION	f_dihedral_angle_d	15.776	5790
X-RAY DIFFRACTION	f_chiral_restr	0.056	1360
X-RAY DIFFRACTION	f_plane_restr	0.005	1675

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7932-1.8135	0.5159	288	0.472	5452	X-RAY DIFFRACTION	65
1.8135-1.8349	0.3348	431	0.3407	8238	X-RAY DIFFRACTION	100
1.8349-1.8573	0.3348	438	0.3098	8355	X-RAY DIFFRACTION	100
1.8573-1.8808	0.2953	436	0.2712	8279	X-RAY DIFFRACTION	100
1.8808-1.9055	0.3016	434	0.2443	8309	X-RAY DIFFRACTION	100
1.9055-1.9316	0.2692	436	0.2197	8277	X-RAY DIFFRACTION	100
1.9316-1.9592	0.219	444	0.1999	8295	X-RAY DIFFRACTION	100
1.9592-1.9885	0.2438	440	0.1913	8360	X-RAY DIFFRACTION	100
1.9885-2.0195	0.2252	433	0.1927	8202	X-RAY DIFFRACTION	100
2.0195-2.0526	0.2085	448	0.1956	8421	X-RAY DIFFRACTION	100
2.0526-2.088	0.2044	421	0.198	8197	X-RAY DIFFRACTION	100
2.088-2.126	0.2122	434	0.1965	8329	X-RAY DIFFRACTION	100
2.126-2.1669	0.2087	441	0.1775	8367	X-RAY DIFFRACTION	100
2.1669-2.2111	0.2058	435	0.1764	8244	X-RAY DIFFRACTION	100
2.2111-2.2592	0.2211	441	0.1779	8301	X-RAY DIFFRACTION	100
2.2592-2.3118	0.1936	428	0.1761	8308	X-RAY DIFFRACTION	100
2.3118-2.3696	0.222	438	0.1703	8298	X-RAY DIFFRACTION	100
2.3696-2.4336	0.1957	433	0.176	8302	X-RAY DIFFRACTION	100
2.4336-2.5052	0.2054	434	0.1744	8323	X-RAY DIFFRACTION	100
2.5052-2.5861	0.1862	438	0.1738	8306	X-RAY DIFFRACTION	100
2.5861-2.6785	0.199	431	0.1718	8299	X-RAY DIFFRACTION	100
2.6785-2.7858	0.2153	436	0.1725	8249	X-RAY DIFFRACTION	100
2.7858-2.9125	0.2128	441	0.179	8296	X-RAY DIFFRACTION	100
2.9125-3.0661	0.1962	443	0.1711	8389	X-RAY DIFFRACTION	100
3.0661-3.2581	0.1855	437	0.172	8264	X-RAY DIFFRACTION	100
3.2581-3.5096	0.1907	446	0.158	8314	X-RAY DIFFRACTION	100
3.5096-3.8627	0.1643	438	0.152	8290	X-RAY DIFFRACTION	100
3.8627-4.4213	0.1584	434	0.1411	8283	X-RAY DIFFRACTION	100
4.4213-5.569	0.1511	431	0.143	8275	X-RAY DIFFRACTION	100
5.569-42.47	0.1978	431	0.1728	8105	X-RAY DIFFRACTION	97

Refinement TLS params.

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

ID	L11 (°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)
1	0.7026	0.0953	-0.1108	0.7365	0.06	0.6421	-0.0449	0.0445	0.0479	-0.0727	0.0373	0.007	-0.049	-0.0058	0.0282	0.1521	-0.0019	-0.0136	0.15	-0.013	0.1779	-15.0171	-18.6281	20.6595
2	1.1443	0.0081	0.0026	1.0282	0.1098	0.7151	0.0075	-0.2192	-0.0477	0.2554	-0.0614	0.0057	-0.0122	-0.0177	0.0254	0.2323	-0.0151	-0.0057	0.2477	0.013	0.1954	20.8516	-11.0184	56.9513

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid -1 through 562)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid -1 through 561)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi