PDB-8q2a: TtX122B - A domain of unknown function from the Teredinibacter tu...

ID or keywords:

Entry

Database: PDB / ID: 8q2a

Title

TtX122B - A domain of unknown function from the Teredinibacter turnerae protein TERTU_2913

Components

Putative lipoprotein

Keywords

UNKNOWN FUNCTION / beta-jelly roll fold / X122 / CAZy / Teredinibacter turnerae

Function / homology

Function and homology information

electron transfer activity / heme binding / metal ion binding
Similarity search - Function

Biological species

Teredinibacter turnerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Rajagopal, B.S. / Hemsworth, G.R.

Funding support

United Kingdom, 1items

Citation

Journal: Iucrj / Year: 2024
Title: Structural dissection of two redox proteins from the shipworm symbiont Teredinibacter turnerae.
Authors: Rajagopal, B.S. / Yates, N. / Smith, J. / Paradisi, A. / Tetard-Jones, C. / Willats, W.G.T. / Marcus, S. / Knox, J.P. / Firdaus-Raih, M. / Henrissat, B. / Davies, G.J. / Walton, P.H. / ...

History

Deposition	Aug 1, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	8q1vC 8q1wC 8q28C 8q29C C: citing same article (ref.)
Similar structure data	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
Related items in Molecule of the Month	#36 - Dec 2002 Cytochrome c similarity (3) #111 - Mar 2009 Hydrogenase similarity (3) #137 - May 2011 Cytochrome bc1 similarity (3) #177 - Sep 2014 Apoptosomes similarity (3) #59 - Nov 2004 Photosystem II similarity (3) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (3) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#36 - Dec 2002
Cytochrome c
similarity (3)
#111 - Mar 2009
Hydrogenase
similarity (3)
#137 - May 2011
Cytochrome bc1
similarity (3)
#177 - Sep 2014
Apoptosomes
similarity (3)
#59 - Nov 2004
Photosystem II
similarity (3)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (3)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Putative lipoprotein

B: Putative lipoprotein

C: Putative lipoprotein

hetero molecules

80.7 kDa, 3 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)	69.141, 75.324, 116.863
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

End auth comp-ID: CYS / End label comp-ID: CYS / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	2 - 235	2 - 235
2	1	1	SER	SER	2 - 235	2 - 235
3	2	2	GLY	GLY	3 - 235	3 - 235
4	2	2	GLY	GLY	3 - 235	3 - 235
5	3	3	GLY	GLY	3 - 235	3 - 235
6	3	3	GLY	GLY	3 - 235	3 - 235

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	Putative lipoprotein Mass: 26867.066 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Teredinibacter turnerae (bacteria) / Gene: TERTU_2913 / Production host: Escherichia coli (E. coli) / References: UniProt: C5BNC6
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density % sol: 34.84 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 25% PEG3350 and 0.1 M Bis-Tris pH 6.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 0.96863 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.96863 Å / Relative weight: 1

Reflection

Resolution: 2.2→46.69 Å / Num. obs: 31699 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC_1/2: 0.601 / R_merge(I) obs: 0.365 / R_pim(I) all: 0.228 / R_rim(I) all: 0.432 / Net I/σ(I): 6.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
9.07-46.69	5.8	0.133	531	0.964	0.08	0.156
2.2-2.27	5.6	2.304	15164	0.726	1.568	2.805

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
Aimless		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→46.69 Å / Cor.coef. F_o:F_c: 0.881 / Cor.coef. F_o:F_c free: 0.836 / SU B: 8.434 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.248
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.259	1583	5.006 %
R_work	0.2085	30041	-
all	0.211	-	-
obs	-	31624	99.694 %

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: 14.89 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.366 Å²	0 Å²	-0 Å²
2-	-	1.98 Å²	-0 Å²
3-	-	-	-0.614 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→46.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5329	0	3	163	5495

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.012	5483
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4694
X-RAY DIFFRACTION	r_angle_refined_deg	2.031	1.636	7479
X-RAY DIFFRACTION	r_angle_other_deg	0.723	1.595	10747
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.816	5	695
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.922	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.435	10	744
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.57	10	291
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	757
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	6850
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1366
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1040
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.207	0.2	4628
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	2672
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.094	0.2	3058
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.186	0.2	191
X-RAY DIFFRACTION	r_metal_ion_refined	0.148	0.2	14
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.179	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.211	0.2	76
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.213	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	2.249	1.433	2792
X-RAY DIFFRACTION	r_mcbond_other	2.248	1.433	2792
X-RAY DIFFRACTION	r_mcangle_it	3.387	2.557	3483
X-RAY DIFFRACTION	r_mcangle_other	3.387	2.558	3484
X-RAY DIFFRACTION	r_scbond_it	3.326	1.643	2691
X-RAY DIFFRACTION	r_scbond_other	3.325	1.644	2692
X-RAY DIFFRACTION	r_scangle_it	5.058	2.874	3996
X-RAY DIFFRACTION	r_scangle_other	5.057	2.875	3997
X-RAY DIFFRACTION	r_lrange_it	6.288	15.337	5999
X-RAY DIFFRACTION	r_lrange_other	6.276	15.347	5990
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.12	0.05	7297
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.116	0.05	7303
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.11	0.05	7298

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	0.11965	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.11965	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.11645	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.11645	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10978	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.10978	0.05008

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 (%)
2.2-2.257	0.52	118	0.483	2141	X-RAY DIFFRACTION	97.7922
2.257-2.319	0.313	119	0.254	2127	X-RAY DIFFRACTION	100
2.319-2.386	0.272	90	0.213	2130	X-RAY DIFFRACTION	100
2.386-2.459	0.311	103	0.211	1980	X-RAY DIFFRACTION	100
2.459-2.539	0.248	109	0.2	1967	X-RAY DIFFRACTION	100
2.539-2.628	0.295	88	0.225	1905	X-RAY DIFFRACTION	99.9499
2.628-2.727	0.314	72	0.258	1841	X-RAY DIFFRACTION	99.3766
2.727-2.838	0.23	90	0.17	1779	X-RAY DIFFRACTION	100
2.838-2.964	0.236	91	0.167	1678	X-RAY DIFFRACTION	100
2.964-3.108	0.232	112	0.158	1605	X-RAY DIFFRACTION	99.9418
3.108-3.275	0.209	65	0.155	1576	X-RAY DIFFRACTION	99.8783
3.275-3.473	0.248	66	0.202	1482	X-RAY DIFFRACTION	99.8066
3.473-3.711	0.23	65	0.18	1379	X-RAY DIFFRACTION	99.7927
3.711-4.006	0.243	83	0.2	1288	X-RAY DIFFRACTION	99.4199
4.006-4.385	0.179	81	0.132	1184	X-RAY DIFFRACTION	100
4.385-4.898	0.157	63	0.131	1098	X-RAY DIFFRACTION	100
4.898-5.645	0.209	49	0.166	975	X-RAY DIFFRACTION	100
5.645-6.888	0.237	61	0.195	828	X-RAY DIFFRACTION	100
6.888-9.638	0.308	28	0.219	673	X-RAY DIFFRACTION	100
9.638-46.69	0.273	30	0.236	405	X-RAY DIFFRACTION	99.5423

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