PDB-9hmu: DUF4465 domain containing protein in complex with vitamin B12.

ID or keywords:

Entry

Database: PDB / ID: 9hmu

Title

DUF4465 domain containing protein in complex with vitamin B12.

Components

DUF4465 domain containing protein D5EK

Keywords

MEMBRANE PROTEIN / Complex / Vitamin B12 / Bacteria / Scavenging / Outer membrane / Membrane associated

Function / homology

PEP-CTERM protein-sorting domain / Protein of unknown function DUF4465 / Domain of unknown function (DUF4465) / CYANOCOBALAMIN / PEP-CTERM protein-sorting domain-containing protein

Function and homology information

Biological species

Coraliomargarita akajimensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Clarke, C. / Banasik, M. / Pickersgill, R.W.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: DUF4465 domains bind vitamin B12.
Authors: Clarke, C. / Banasik, M. / Pickersgill, R.W.

History

Deposition	Dec 9, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jan 22, 2025	Group: Structure summary / Category: entity / Item: _entity.pdbx_description

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9hmu.cif.gz	617.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9hmu.ent.gz	423.3 KB	Display	PDB format
PDBx/mmJSON format	9hmu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9hmu_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	9hmu_full_validation.pdf.gz	3.3 MB	Display
Data in XML	9hmu_validation.xml.gz	40.2 KB	Display
Data in CIF	9hmu_validation.cif.gz	54.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hm/9hmu ftp://data.pdbj.org/pub/pdb/validation_reports/hm/9hmu	HTTPS FTP

-
Related structure data

Related structure data	9fct
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: DUF4465 domain containing protein D5EK

B: DUF4465 domain containing protein D5EK

C: DUF4465 domain containing protein D5EK

hetero molecules

85 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DUF4465 domain containing protein D5EK

hetero molecules

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

2

B: DUF4465 domain containing protein D5EK

hetero molecules

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

3

C: DUF4465 domain containing protein D5EK

hetero molecules

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

Unit cell

Length a, b, c (Å)	113.72, 113.72, 162.593
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	154
Space group name H-M	P3₂21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	B
6	3	C

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	A	A	28 - 249	28 - 249
2	1	1	PRO	PRO	B	B	28 - 249	28 - 249
3	2	2	PRO	PRO	A	A	28 - 249	28 - 249
4	2	2	PRO	PRO	C	C	28 - 249	28 - 249
5	3	3	GLU	GLU	B	B	28 - 250	28 - 250
6	3	3	GLU	GLU	C	C	28 - 250	28 - 250

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	DUF4465 domain containing protein D5EK Mass: 26946.217 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: His-tagged, C-term domain removed/truncated wild type Source: (gene. exp.) Coraliomargarita akajimensis (bacteria) Gene: Caka_1781 / Production host: Escherichia coli (E. coli) / References: UniProt: D5EK51
#2: Chemical	ChemComp-CNC / CYANOCOBALAMIN Mass: 1356.373 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆₃H₈₉CoN₁₄O₁₄P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.5 % / Description: Dark red, cubic crystals
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 35% (poly acrylic acid sodium salt) 2100 0.1M HEPES (pH 7.5) 0.2M ammonium sulfate

-
Data collection

Diffraction	Mean temperature: 77.36 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9655 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 22, 2024
Radiation	Monochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9655 Å / Relative weight: 1
Reflection	Resolution: 1.8→84.379 Å / Num. obs: 96344 / % possible obs: 92.1 % / Redundancy: 12.8 % / CC_1/2: 0.907 / R_merge(I) obs: 0.131 / R_pim(I) all: 0.091 / R_rim(I) all: 0.147 / Net I/σ(I): 9.3
Reflection shell	Resolution: 1.849→1.879 Å / Redundancy: 1.299 % / R_merge(I) obs: 1.362 / Mean I/σ(I) obs: 1 / Num. unique obs: 20050 / CC_1/2: 0.373 / R_pim(I) all: 0.964 / R_rim(I) all: 0.751 / % possible all: 96.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→84.379 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.941 / SU B: 6.991 / SU ML: 0.099 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2132	4618	4.818 %
R_work	0.1896	91226	-
all	0.191	-	-
obs	-	95844	92.077 %

Solvent computation

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

Displacement parameters

B_iso mean: 28.324 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.298 Å²	-0.149 Å²	-0 Å²
2-	-	-0.298 Å²	0 Å²
3-	-	-	0.965 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→84.379 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5126	0	282	665	6073

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	5567
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.015	4751
X-RAY DIFFRACTION	r_angle_refined_deg	2.198	1.848	7684
X-RAY DIFFRACTION	r_angle_other_deg	0.837	1.771	10889
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.596	5	667
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.678	5	15
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.906	10	720
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.691	10	252
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	814
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	6724
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1408
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	798
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.16	0.2	4462
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	2790
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2749
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	511
X-RAY DIFFRACTION	r_metal_ion_refined	0.077	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.071	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.156	0.2	38
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.17	0.2	35
X-RAY DIFFRACTION	r_mcbond_it	1.603	1.863	2677
X-RAY DIFFRACTION	r_mcbond_other	1.603	1.863	2677
X-RAY DIFFRACTION	r_mcangle_it	2.446	3.337	3341
X-RAY DIFFRACTION	r_mcangle_other	2.445	3.339	3342
X-RAY DIFFRACTION	r_scbond_it	2.071	2.003	2890
X-RAY DIFFRACTION	r_scbond_other	2.071	2.003	2891
X-RAY DIFFRACTION	r_scangle_it	3.038	3.627	4343
X-RAY DIFFRACTION	r_scangle_other	3.038	3.627	4344
X-RAY DIFFRACTION	r_lrange_it	5.792	22.153	6291
X-RAY DIFFRACTION	r_lrange_other	5.528	19.454	6099
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.057	0.05	7235
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.064	0.05	7150
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.066	0.05	7194

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.05691	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.05691	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.0644	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.0644	0.05009
3	5	B	X-RAY DIFFRACTION	Local ncs	0.06552	0.05009
3	6	C	X-RAY DIFFRACTION	Local ncs	0.06552	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.85-1.898	0.326	327	0.326	5864	0.326	7618	0.899	0.892	81.2681	0.327
1.898-1.95	0.353	256	0.354	5306	0.354	7417	0.684	0.732	74.9899	0.371
1.95-2.007	0.284	339	0.283	6514	0.283	7211	0.912	0.918	95.0354	0.281
2.007-2.068	0.274	261	0.239	6374	0.241	7053	0.942	0.958	94.0734	0.222
2.068-2.136	0.301	296	0.277	5919	0.278	6810	0.875	0.886	91.2628	0.269
2.136-2.211	0.231	295	0.198	6224	0.199	6569	0.966	0.974	99.2388	0.166
2.211-2.294	0.259	285	0.24	5311	0.241	6372	0.898	0.911	87.8217	0.21
2.294-2.388	0.2	287	0.188	5785	0.188	6132	0.976	0.979	99.0215	0.151
2.388-2.494	0.23	282	0.189	5531	0.191	5883	0.97	0.98	98.8101	0.147
2.494-2.616	0.241	285	0.199	5274	0.201	5634	0.968	0.978	98.6688	0.157
2.616-2.757	0.278	234	0.217	4250	0.221	5401	0.87	0.953	83.0217	0.172
2.757-2.924	0.237	259	0.189	4756	0.191	5087	0.961	0.978	98.5846	0.153
2.924-3.126	0.21	228	0.177	4440	0.178	4772	0.973	0.981	97.8206	0.145
3.126-3.376	0.162	185	0.153	4192	0.153	4465	0.984	0.987	98.0291	0.134
3.376-3.697	0.176	152	0.158	3213	0.159	4136	0.985	0.987	81.3588	0.145
3.697-4.133	0.174	183	0.149	3277	0.151	3765	0.984	0.988	91.8991	0.143
4.133-4.77	0.149	167	0.127	3075	0.128	3325	0.987	0.991	97.5038	0.127
4.77-5.838	0.146	147	0.134	2633	0.134	2851	0.99	0.991	97.5096	0.135
5.838-8.236	0.163	90	0.159	2072	0.159	2242	0.986	0.986	96.4318	0.159
8.236-84.379	0.179	60	0.18	1184	0.18	1314	0.98	0.982	94.6728	0.192

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	0.8579	0.1298	-0.0162	2.0553	0.1307	1.6315	-0.0477	0.0494	-0.0572	-0.1883	-0.0183	0.0958	0.1948	-0.0317	0.066	0.0698	-0.0061	-0.0021	0.0201	0.0098	0.0258	44.9736	6.721	3.355
2	1.6214	-0.595	-0.2176	1.2414	0.0533	1.1247	0.0584	0.1252	-0.078	-0.138	-0.0277	0.0402	0.0653	0.0021	-0.0307	0.0312	0.0226	-0.0065	0.0421	-0.0061	0.0054	31.1394	36.2474	-16.93
3	1.2202	0.2732	-0.1172	1.3067	0.1944	1.379	0.034	-0.1668	-0.0562	0.0877	-0.0433	-0.0356	0.0768	0.0438	0.0094	0.0097	-0.0029	-0.0027	0.051	-0.0025	0.0071	68.4335	24.5388	-18.7298

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	27 - 301
2	X-RAY DIFFRACTION	2	ALL	B	28 - 301
3	X-RAY DIFFRACTION	3	ALL	C	28 - 301

-
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