PDB-3rpd: The structure of a B12-independent methionine synthase from Shewa...

ID or keywords:

Entry

Database: PDB / ID: 3rpd

Title

The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.

Components

Methionine synthase (B12-independent)

Keywords

TRANSFERASE /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG /

Rossmann Fold /

methionine synthase / Zn

Function / homology

Function and homology information

5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase /

5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / methionine biosynthetic process /

methylation / zinc ion binding
Similarity search - Function

Biological species

Shewanella sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD /

MAD / Resolution: 1.5 Å

Authors

Cuff, M.E. / Li, H. / Hatzos-Skintges, C. / Tesar, C. / Bearden, J. / Clancy, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.
Authors: Cuff, M.E. / Li, H. / Hatzos-Skintges, C. / Tesar, C. / Bearden, J. / Clancy, A. / Joachimiak, A.

History

Deposition	Apr 26, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 31, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3rpd.cif.gz	311.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3rpd.ent.gz	262.8 KB	Display	PDB format
PDBx/mmJSON format	3rpd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	3atz-3 5tty-d 4e2d-1 4jip-d 1vji-d 4tuf-2 6dvn-1 5z3c-d 3cix-d 5z3b-d 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
Other databases	TargetDB: apc100174

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Methionine synthase (B12-independent)

B: Methionine synthase (B12-independent)

hetero molecules

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

1

A: Methionine synthase (B12-independent)

hetero molecules

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

2

B: Methionine synthase (B12-independent)

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.099, 89.371, 86.526
Angle α, β, γ (deg.)	90.000, 92.450, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Methionine synthase (B12-independent) Mass: 40574.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella sp. (bacteria) / Strain: W3-18-1 / Gene: Sputw3181_1250 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A1RHE8, UniProt: A0A6N3J2K5*PLUS, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-MSE / SELENOMETHIONINE / Selenomethionine Type: L-peptide linking / Mass: 196.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₁NO₂Se
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 944 / 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: 2.19 Å³/Da / Density % sol: 43.95 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Imidazole:HCl pH 8.0, 1.0M Sodium Citrate Tribasic, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97942 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97942 Å / Relative weight: 1

Reflection

Redundancy: 4.4 % / Av σ(I) over netI: 23.92 / Number: 491490 / R_merge(I) obs: 0.088 / Χ²: 1.8 / D res high: 1.5 Å / D res low: 50 Å / Num. obs: 111443 / % possible obs: 99.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.07	50	98.3	1	0.071	5.756	4.4
3.23	4.07	99.5	1	0.063	3.862	4.4
2.82	3.23	100	1	0.075	3.542	4.5
2.56	2.82	100	1	0.083	3.129	4.6
2.38	2.56	99.8	1	0.086	2.645	4.5
2.24	2.38	99.5	1	0.087	2.24	4.5
2.13	2.24	99.2	1	0.092	1.993	4.4
2.04	2.13	98.8	1	0.097	1.763	4.5
1.96	2.04	98.4	1	0.11	1.496	4.4
1.89	1.96	99.1	1	0.123	1.301	4.4
1.83	1.89	99	1	0.14	1.136	4.4
1.78	1.83	99	1	0.161	0.999	4.4
1.73	1.78	99.1	1	0.184	0.877	4.4
1.69	1.73	99.2	1	0.209	0.785	4.4
1.65	1.69	99.6	1	0.23	0.736	4.4
1.62	1.65	99.1	1	0.268	0.706	4.4
1.58	1.62	99.4	1	0.29	0.651	4.4
1.55	1.58	99.6	1	0.325	0.635	4.4
1.53	1.55	99.3	1	0.372	0.624	4.4
1.5	1.53	98.8	1	0.425	0.614	4.1

Reflection

Resolution: 1.5→50 Å / Num. all: 111443 / Num. obs: 111443 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / R_merge(I) obs: 0.088 / Net I/σ(I): 8.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	% possible all
1.5-1.53	4.1	0.425	98.8
1.53-1.55	4.4	0.372	99.3
1.55-1.58	4.4	0.325	99.6
1.58-1.62	4.4	0.29	99.4
1.62-1.65	4.4	0.268	99.1
1.65-1.69	4.4	0.23	99.6
1.69-1.73	4.4	0.209	99.2
1.73-1.78	4.4	0.184	99.1
1.78-1.83	4.4	0.161	99
1.83-1.89	4.4	0.14	99
1.89-1.96	4.4	0.123	99.1
1.96-2.04	4.4	0.11	98.4
2.04-2.13	4.5	0.097	98.8
2.13-2.24	4.4	0.092	99.2
2.24-2.38	4.5	0.087	99.5
2.38-2.56	4.5	0.086	99.8
2.56-2.82	4.6	0.083	100
2.82-3.23	4.5	0.075	100
3.23-4.07	4.4	0.063	99.5
4.07-50	4.4	0.071	98.3

-
Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2 Å / D res low: 50 Å / FOM : 0.387 / FOM acentric: 0.4 / FOM centric: 0 / Reflection: 47424 / Reflection acentric: 45870 / Reflection centric: 1554

Phasing MAD set

R cullis acentric: 1.42 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.2 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 45870 / Reflection centric: 1554

Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)	R cullis acentric	Loc acentric	Loc centric	Reflection acentric	Reflection centric
12.5-50	1.51	0.3	0.2	162	34
7.14-12.5	1.37	0.3	0.2	788	81
5-7.14	1.63	0.3	0.2	1896	127
3.85-5	1.02	0.2	0.2	3465	164
3.13-3.85	1.11	0.2	0.2	5578	221
2.63-3.13	1.49	0.2	0.1	8115	264
2.27-2.63	1.62	0.2	0.1	11183	310
2-2.27	1.56	0.2	0.1	14683	353

Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

ID	B iso	Fract x	Fract y	Fract z	Occupancy
1	8.2291	-0.167	-0.671	-0.004	4.912
2	10.0233	-0.072	-0.713	0.327	4.561
3	8.9183	-0.391	-0.632	-0.089	3.718
4	10.7836	-0.321	-0.501	-0.105	3.924
5	8.69	0.081	-0.531	0.403	3.524
6	12.316	0.153	-0.662	0.405	3.476
7	31.8865	-0.427	-0.582	-0.219	3.825
8	14.5077	0.138	-0.696	0.261	2.96
9	50.3734	0.192	-0.597	0.527	3.835
10	17.0174	-0.348	-0.661	0.072	1.866
11	50.4192	-0.626	-0.46	-0.082	3.303
12	11.3476	0.189	-0.642	0.41	1.584
13	6.2454	-0.428	-0.613	-0.097	1.628
14	44.7017	0.382	-0.491	0.373	2.317

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	Reflection	Reflection acentric	Reflection centric
12.5-50	0.233	0.282	196	162	34
7.14-12.5	0.398	0.439	869	788	81
5-7.14	0.442	0.471	2023	1896	127
3.85-5	0.357	0.374	3629	3465	164
3.13-3.85	0.389	0.405	5799	5578	221
2.63-3.13	0.406	0.419	8379	8115	264
2.27-2.63	0.403	0.415	11493	11183	310
2-2.27	0.365	0.374	15036	14683	353

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 111310

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.13-100	60.9	0.781	721
5.75-8.13	58.7	0.893	1314
4.69-5.75	59.9	0.915	1695
4.07-4.69	61.7	0.922	1998
3.64-4.07	62.5	0.912	2243
3.32-3.64	62.3	0.904	2469
3.07-3.32	63.7	0.884	2708
2.87-3.07	63.3	0.876	2897
2.71-2.87	62.1	0.886	3084
2.57-2.71	61.9	0.875	3264
2.45-2.57	61.9	0.881	3457
2.35-2.45	61.6	0.877	3538
2.26-2.35	61	0.873	3772
2.17-2.26	62.6	0.876	3873
2.1-2.17	64	0.871	3991
2.03-2.1	64.4	0.865	4171
1.97-2.03	76.7	0.85	4272
1.92-1.97	90.5	0.835	4403
1.87-1.92	87.1	0.825	4541
1.82-1.87	89.1	0.825	4655
1.77-1.82	90.1	0.819	4750
1.73-1.77	89.3	0.809	4912
1.7-1.73	89.9	0.8	4971
1.66-1.7	90.1	0.797	5112
1.63-1.66	90.3	0.782	5192
1.59-1.63	89.5	0.771	5295
1.56-1.59	89.2	0.733	5450
1.54-1.56	92.2	0.699	5488
1.5-1.54	89.9	0.54	7074

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6.1	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.5→36.5 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.188 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0716 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.189	5565	5 %	RANDOM
R_work	0.16362	-	-	-
obs	0.1649	105371	99.14 %	-
all	-	110936	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 12.229 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.33 Å²	0 Å²	0.54 Å²
2-	-	-0.17 Å²	0 Å²
3-	-	-	0.55 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→36.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5438	0	38	944	6420

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	5668
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3867
X-RAY DIFFRACTION	r_angle_refined_deg	1.425	1.967	7692
X-RAY DIFFRACTION	r_angle_other_deg	0.905	3	9496
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.326	5	706
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.69	24.859	249
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.735	15	1028
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.315	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	870
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	6241
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1076
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.762	1.5	3487
X-RAY DIFFRACTION	r_mcbond_other	0.229	1.5	1399
X-RAY DIFFRACTION	r_mcangle_it	1.361	2	5657
X-RAY DIFFRACTION	r_scbond_it	2.347	3	2181
X-RAY DIFFRACTION	r_scangle_it	3.757	4.5	2032
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.5→1.539 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.219	410	-
R_work	0.198	7787	-
obs	-	-	98.93 %

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	0.3707	0.1799	-0.0143	0.3643	0.0281	0.2785	-0.0042	0.038	-0.0118	0.0129	-0.0047	-0.0199	-0.0039	0.0137	0.0089	0.0237	0.0098	-0.0055	0.0305	0.002	0.0032	2.1676	33.6449	35.5847
2	0.4573	-0.1286	-0.0012	0.2918	-0.0596	0.312	0.006	0.016	0.0151	-0.0253	-0.0054	0.0034	-0.0008	-0.0085	-0.0006	0.018	-0.0052	-0.0069	0.0156	-0.0011	0.0097	-18.0337	35.9092	78.1541

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 9999
2	X-RAY DIFFRACTION	2	B	-10 - 9999

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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