PDB-3wva: SeMet-labelled HcgF from Methanocaldococcus jannaschii

ID or keywords:

Entry

Database: PDB / ID: 3wva

Title

SeMet-labelled HcgF from Methanocaldococcus jannaschii

Components

UPF0254 protein MJ1251

Keywords

HYDROLASE /

Thioesterase

Function / homology

FeGP cofactor biosynthesis protein HcgF / FeGP cofactor biosynthesis protein HcgF / UPF0254 protein MJ1251

Function and homology information

Biological species

Methanocaldococcus jannaschii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.4 Å

Authors

Fujishiro, T. / Ermler, U. / Shima, S.

Citation

Journal: Nat Commun / Year: 2015
Title: Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor
Authors: Fujishiro, T. / Kahnt, J. / Ermler, U. / Shima, S.

History

Deposition	May 16, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 29, 2015	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3wva.cif.gz	147.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3wva.ent.gz	123.4 KB	Display	PDB format
PDBx/mmJSON format	3wva.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wv/3wva ftp://data.pdbj.org/pub/pdb/validation_reports/wv/3wva	HTTPS FTP

-
Related structure data

Related structure data	3wv7C 3wv8C 3wv9C 3wvbC 3wvcC C: citing same article (ref.)
Similar structure data	3wvb-d 3ur8-2 2nxf-d 6q4l-d 6jms-d 6d3a-1 4ggd-1 6qvs-2 3s25-d 6ui3-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: UPF0254 protein MJ1251

B: UPF0254 protein MJ1251

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	45.010, 72.730, 45.630
Angle α, β, γ (deg.)	90.000, 102.610, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	1 - 167
2	0	1	0	B	1 - 167

#1: Protein	UPF0254 protein MJ1251 Mass: 19441.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ1251 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star References: UniProt: Q58649, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

UPF0254 protein MJ1251

Mass: 19441.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1251 / Plasmid: pET28b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
References: UniProt: Q58649,

Hydrolases; Acting on ester bonds; Thioester hydrolases

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 357 / 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: 1.87 Å³/Da / Density % sol: 34.38 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20%(w/v)PEG3000, 200mM sodium chloride, 100mM HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 0.972, 0.9791, 0.9798

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2011

Radiation

Monochromator: A Si(111) double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.972	1
2	0.9791	1
3	0.9798	1

Reflection

Resolution: 1.15→50 Å / Num. obs: 57849 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3 % / B_iso Wilson estimate: 16.887 Å² / R_merge(I) obs: 0.044 / Χ²: 1.028 / Net I/σ(I): 12.84

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.15-1.25		0.574	0.376	2.99	51075	23113	19732	0.467	85.4
1.25-1.4		0.3	0.208	5.87	70496	23475	23357	0.254	99.5
1.4-1.6		0.125	0.101	10.92	59498	19152	19087	0.123	99.7
1.6-1.95		0.057	0.056	17.52	55382	17410	17313	0.067	99.4
1.95-2.5		0.031	0.038	25.8	36374	11347	11250	0.046	99.1
2.5-3.1		0.028	0.035	27.49	14694	4912	4831	0.043	98.4
3.1-4.1		0.024	0.033	31.9	9942	3067	3032	0.04	98.9
4.1-6		0.025	0.033	28.81	4614	1604	1564	0.04	97.5
6-8		0.027	0.04	30.21	1438	446	443	0.047	99.3
8-12		0.027	0.043	30.34	762	236	233	0.051	98.7
	12	0.031	0.044	28.59	290	103	96	0.053	93.2

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
REFMAC	5.8.0071	refinement
PDB_EXTRACT	3.14	data extraction
XDS		data scaling
XDS		data reduction
SHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 1.4→37.98 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.953 / SU B: 1.804 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1903	2665	5.1 %	RANDOM
R_work	0.1489	-	-	-
obs	0.151	52380	92.81 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 51.63 Å² / B_iso mean: 14.399 Å² / B_iso min: 5.78 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→37.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2668	0	0	357	3025

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.026	0.019	2799
X-RAY DIFFRACTION	r_angle_refined_deg	2.449	1.993	3779
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.239	5	360
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.588	25.041	121
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.168	15	526
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.48	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.184	0.2	429
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	2054
X-RAY DIFFRACTION	r_mcbond_it	1.037	0.754	1370
X-RAY DIFFRACTION	r_mcangle_it	1.458	1.133	1717
X-RAY DIFFRACTION	r_scbond_it	2.554	1.072	1429

Refine LS restraints NCS

Ens-ID: 1 / Number: 226 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.4→1.436 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.213	113	-
R_work	0.159	2289	-
all	-	2402	-
obs	-	-	57.91 %

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	1.4613	-0.4228	-0.5842	0.5891	0.2429	0.7783	0.0089	0.0366	0.019	0.0065	-0.0046	-0.0127	0.0029	-0.0135	-0.0044	0.01	0.0016	-0.0042	0.0045	-0.0055	0.0106	16.8577	20.6215	36.6894
2	1.6182	-0.6151	0.6319	2.9561	-1.6729	1.8764	0.0046	0.0822	0.0814	0.0099	0.0243	-0.0868	-0.0631	0.0125	-0.0289	0.0068	-0.0018	0.0076	0.0298	0.0091	0.0181	26.2993	26.2285	30.7809
3	0.9968	-0.4061	-0.0256	0.5711	0.1116	0.3965	-0.0384	-0.1168	-0.0322	0.0757	0.0363	0.0408	0.0215	-0.0123	0.002	0.0176	0.0073	-0.0008	0.0176	-0.0009	0.0083	8.2013	20.2528	45.3432
4	3.985	-0.8372	0.6322	0.5941	0.0713	0.5428	0.0432	0.1045	0.1649	-0.0529	-0.0258	-0.0391	0.0222	0.0361	-0.0174	0.0133	-0.0007	-0.001	0.0089	0.0005	0.0122	14.2244	29.8069	38.8902
5	2.4366	-0.4213	-0.3647	0.5666	0.2687	0.4424	0.0089	0.0405	0.067	-0.0146	-0.0206	0.0148	-0.0202	-0.0114	0.0117	0.0072	0.0009	-0.0025	0.0116	-0.0119	0.018	7.0898	12.6401	28.1668
6	1.1184	0.86	-0.9153	2.3478	-1.9767	3.0652	-0.0534	0.1269	0.0727	-0.1485	-0.0306	-0.0151	0.0105	-0.1199	0.084	0.0259	0.0205	-0.0115	0.0454	0.0037	0.0713	-2.3223	18.6893	22.696
7	0.2816	-0.5872	0.1244	1.2575	-0.3673	0.5679	0.011	0.0124	0.0049	-0.032	-0.0532	-0.0259	0.0199	0.0307	0.0421	0.038	-0.0049	0.0015	0.041	0.0018	0.0535	16.1895	5.7604	36.0506
8	1.1314	0.6268	0.3965	4.6962	1.1259	0.3328	-0.1444	-0.0469	-0.0548	0.1467	0.1799	-0.0029	-0.0046	0.0367	-0.0355	0.031	0.0095	0.0146	0.0477	-0.0151	0.0669	29.1586	7.4143	29.2851
9	1.5844	0.1599	-0.4905	0.3436	0.0228	0.5013	-0.0256	0.0999	-0.0346	0.0008	-0.0171	0.0206	-0.0061	-0.0338	0.0427	0.0139	-0.0044	0.0005	0.0165	-0.0153	0.0217	11.6015	5.6422	22.5054

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 20
2	X-RAY DIFFRACTION	2	A	21 - 47
3	X-RAY DIFFRACTION	3	A	48 - 136
4	X-RAY DIFFRACTION	4	A	137 - 167
5	X-RAY DIFFRACTION	5	B	1 - 20
6	X-RAY DIFFRACTION	6	B	21 - 47
7	X-RAY DIFFRACTION	7	B	48 - 69
8	X-RAY DIFFRACTION	8	B	70 - 79
9	X-RAY DIFFRACTION	9	B	80 - 167

-
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://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