PDB-6h9l: Kcr_0859 delta TM from Korarchaeum cryptofilum

ID or keywords:

Entry

Database: PDB / ID: 6h9l

Title

Kcr_0859 delta TM from Korarchaeum cryptofilum

Components

Uncharacterized protein

Keywords

MEMBRANE PROTEIN / coiled coil / beta-layer

Function / homology

membrane / DUF1640 domain-containing protein

Function and homology information

Biological species

Korarchaeum cryptofilum

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.19 Å

Authors

Hartmann, M.D. / Lupas, A.N. / Hernandez Alvarez, B.

Citation

Journal: Structure / Year: 2019
Title: Characterization of MCU-Binding Proteins MCUR1 and CCDC90B - Representatives of a Protein Family Conserved in Prokaryotes and Eukaryotic Organelles.
Authors: Adlakha, J. / Karamichali, I. / Sangwallek, J. / Deiss, S. / Bar, K. / Coles, M. / Hartmann, M.D. / Lupas, A.N. / Hernandez Alvarez, B.

History

Deposition	Aug 4, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2019	Group: Data collection / Database references Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Nov 13, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6h9l.cif.gz	167.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6h9l.ent.gz	134.3 KB	Display	PDB format
PDBx/mmJSON format	6h9l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h9/6h9l ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h9l	HTTPS FTP

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Related structure data

Related structure data	6h9mC C: citing same article (ref.)
Similar structure data	4cii-d 4oia-2 6xi3-d 4oia-1 4cc1-1 4xa1-2 4cc1-2 2kui-d 4cbz-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	197.520, 48.880, 51.060
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	B
2	3	C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	ASP	ASP	A	A	2 - 127	5 - 130
2	1	SER	SER	ASP	ASP	B	B	2 - 127	5 - 130
1	2	ASN	ASN	ASP	ASP	A	A	3 - 127	6 - 130
2	2	ASN	ASN	ASP	ASP	C	C	3 - 127	6 - 130
1	3	ASN	ASN	ARG	ARG	B	B	3 - 129	6 - 132
2	3	ASN	ASN	ARG	ARG	C	C	3 - 129	6 - 132

NCS ensembles :

ID
1
2
3

#1: Protein	Uncharacterized protein Mass: 16333.117 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Korarchaeum cryptofilum (strain OPF8) (archaea) Gene: Kcr_0859 / Production host: Escherichia coli (E. coli) / References: UniProt: B1L576
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.52 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium cacodylate pH 6.5, 30% MPD, 5% PEG 2000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97895 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97895 Å / Relative weight: 1
Reflection	Resolution: 2.19→39.3 Å / Num. obs: 26105 / % possible obs: 99 % / Redundancy: 3.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.086 / Net I/σ(I): 9.23
Reflection shell	Resolution: 2.19→2.32 Å / Redundancy: 3.27 % / R_merge(I) obs: 0.585 / Mean I/σ(I) obs: 1.74 / CC_1/2: 0.798 / % possible all: 95.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XDS		data reduction
XDS		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.19→39.3 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.906 / SU B: 13.628 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.221 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27331	1299	5 %	RANDOM
R_work	0.24262	-	-	-
obs	0.24417	24806	99.39 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 48.116 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2 Å²	-0 Å²	0 Å²
2-	-	2.28 Å²	0 Å²
3-	-	-	-4.29 Å²

Refinement step

Cycle: 1 / Resolution: 2.19→39.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3102	0	0	121	3223

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	3126
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	3192
X-RAY DIFFRACTION	r_angle_refined_deg	1.036	2.027	4185
X-RAY DIFFRACTION	r_angle_other_deg	1.099	3	7342
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.899	5	385
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.868	23.988	163
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.209	15	664
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.457	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	496
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3430
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	612
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	0.992	3.347	1537
X-RAY DIFFRACTION	r_mcbond_other	0.988	3.345	1536
X-RAY DIFFRACTION	r_mcangle_it	1.599	5.004	1917
X-RAY DIFFRACTION	r_mcangle_other	1.598	5.007	1918
X-RAY DIFFRACTION	r_scbond_it	1.545	3.609	1589
X-RAY DIFFRACTION	r_scbond_other	1.544	3.61	1590
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.514	5.329	2267
X-RAY DIFFRACTION	r_long_range_B_refined	4.41	25.863	3679
X-RAY DIFFRACTION	r_long_range_B_other	4.385	25.757	3644
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	6040	0.17
1	2	B	6040	0.17
2	1	A	6143	0.17
2	2	C	6143	0.17
3	1	B	5880	0.19
3	2	C	5880	0.19

LS refinement shell

Resolution: 2.194→2.25 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.333	84	-
R_work	0.317	1685	-
obs	-	-	93.15 %

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	0.1865	-0.617	-0.1861	3.49	3.5638	7.643	0.0073	-0.0403	-0.1222	0.066	0.0886	0.1867	0.2434	-0.0777	-0.0959	0.0875	-0.0766	0.0352	0.1072	0.0079	0.1794	19.566	-21.087	104.8568
2	6.7399	6.5904	0.2958	6.8557	1.0012	1.3578	0.084	0.2968	0.0148	0.1045	0.0572	-0.0202	-0.0258	-0.3228	-0.1412	0.0364	-0.0319	0.0046	0.1637	-0.0152	0.2008	26.3238	-13.6983	94.3285
3	4.2509	-4.1173	-2.6859	4.68	1.9521	2.3098	0.0381	-0.169	0.2117	-0.0575	0.1295	-0.1417	0.0086	0.1337	-0.1676	0.1204	-0.0066	0.0299	0.0827	-0.0433	0.1811	43.9401	-4.1283	95.2066
4	2.0375	-0.3175	-3.6243	0.0836	0.4962	6.9279	0.1243	-0.0143	0.0609	0.0164	-0.0235	-0.0196	-0.2112	0.1918	-0.1008	0.0974	-0.0024	0.0602	0.1621	-0.0158	0.1554	76.4257	-5.7557	30.3486
5	2.0848	2.0628	2.7555	13.2955	1.2703	4.8176	-0.1567	0.0188	0.1176	-0.0084	0.3453	-0.0477	0.0133	-0.26	-0.1886	0.0795	-0.04	-0.082	0.1967	0.0305	0.2393	15.108	-13.0255	95.7709
6	7.9539	-2.4151	3.4323	3.4136	-1.3203	1.6776	0.0441	0.0081	0.2603	0.1007	-0.0008	0.1338	-0.1778	0.0475	-0.0433	0.2328	-0.0085	0.1405	0.0995	-0.0381	0.1783	27.6416	-5.4554	101.8311
7	0.0857	0.0498	-0.538	1.2296	-0.4424	3.5359	-0.013	0.0165	-0.0673	0.0894	-0.2819	-0.073	-0.1281	-0.049	0.2949	0.1087	-0.0141	0.045	0.143	-0.0089	0.1878	41.9753	-15.0065	96.5184
8	1.9604	-0.2084	-3.7575	0.0618	0.338	7.593	-0.0625	-0.0044	-0.0593	0.022	-0.0627	-0.013	0.1474	0.1617	0.1252	0.0957	0.0532	0.0531	0.1857	0.0347	0.1485	78.3811	-15.8124	31.2998
9	5.0798	0.4292	5.0466	6.6774	-4.2469	8.3034	0.4973	-0.3603	0.254	0.3424	-0.0949	0.9197	0.2866	-0.3219	-0.4024	0.1138	-0.0036	0.1369	0.1861	-0.0473	0.2742	18.4932	-7.8972	107.8069
10	1.6063	-1.339	-2.9695	1.9879	2.9923	8.5837	-0.0684	-0.109	-0.2904	0.0147	-0.039	0.1989	0.0533	-0.0102	0.1075	0.0802	-0.0141	0.0427	0.1174	0.0119	0.1568	30.0334	-16.0418	103.3924
11	2.1271	3.5594	-0.921	7.9468	-2.2904	0.9729	0.0521	0.0854	-0.0198	-0.1349	-0.0042	0.0134	-0.0594	-0.0964	-0.0479	0.1112	0.0198	0.007	0.1243	-0.0102	0.1352	37.2869	-9.4252	86.0169
12	1.7979	-0.1603	-3.2575	0.0592	0.1743	6.5593	0.0149	0.1242	0.0394	0.0166	-0.031	-0.0174	0.079	-0.0439	0.0161	0.0784	0.0307	0.048	0.2009	-0.003	0.1374	69.9131	-12.7759	26.5014

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 13
2	X-RAY DIFFRACTION	2	A	14 - 31
3	X-RAY DIFFRACTION	3	A	32 - 47
4	X-RAY DIFFRACTION	4	A	48 - 128
5	X-RAY DIFFRACTION	5	B	2 - 13
6	X-RAY DIFFRACTION	6	B	14 - 31
7	X-RAY DIFFRACTION	7	B	32 - 47
8	X-RAY DIFFRACTION	8	B	48 - 130
9	X-RAY DIFFRACTION	9	C	3 - 13
10	X-RAY DIFFRACTION	10	C	14 - 31
11	X-RAY DIFFRACTION	11	C	32 - 47
12	X-RAY DIFFRACTION	12	C	48 - 130

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