PDB-6x1h: Crystal structure of a guanine nucleotide exchange factor (GEF) d...

ID or keywords:

Entry

Database: PDB / ID: 6x1h

Title

Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB

Components

ULP_PROTEASE domain-containing protein

Keywords

SIGNALING PROTEIN /

guanine nucleotide exchange factor / GEF /

Orientia tsutsugamushi / scrub typhus

Function / homology

Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily /

proteolysis / NICKEL (II) ION / Ubiquitin-like protease family profile domain-containing protein

Function and homology information

Biological species

Orientia tsutsugamushi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.91 Å

Authors

Lim, C.S. / Xiong, Y.

Funding support

United States, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Crystal structure of a guanine nucleotide exchange factor encoded by the scrub typhus pathogen Orientia tsutsugamushi .
Authors: Lim, C. / Berk, J.M. / Blaise, A. / Bircher, J. / Koleske, A.J. / Hochstrasser, M. / Xiong, Y.

History

Deposition	May 18, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 16, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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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Download

PDBx/mmCIF format	6x1h.cif.gz	524 KB	Display	PDBx/mmCIF format
PDB format	pdb6x1h.ent.gz	440.7 KB	Display	PDB format
PDBx/mmJSON format	6x1h.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/x1/6x1h ftp://data.pdbj.org/pub/pdb/validation_reports/x1/6x1h	HTTPS FTP

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Related structure data

Related structure data	6x1gSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4iap-1 1y19-5 2nyk-d 1y19-2 1in7-d 1y19-3 1in8-d 1idr-d 3qf3-2 1y19-6 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

6x1gSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

E: ULP_PROTEASE domain-containing protein

D: ULP_PROTEASE domain-containing protein

B: ULP_PROTEASE domain-containing protein

F: ULP_PROTEASE domain-containing protein

C: ULP_PROTEASE domain-containing protein

A: ULP_PROTEASE domain-containing protein

hetero molecules

151 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

E: ULP_PROTEASE domain-containing protein

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

2

D: ULP_PROTEASE domain-containing protein

hetero molecules

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

3

B: ULP_PROTEASE domain-containing protein

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

4

F: ULP_PROTEASE domain-containing protein

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

5

C: ULP_PROTEASE domain-containing protein

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

6

A: ULP_PROTEASE domain-containing protein

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

Unit cell

Length a, b, c (Å)	110.533, 110.533, 251.240
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃

Components on special symmetry positions

ID	Model	Components
1	1	D-801- NI

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: 0

Dom-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	HIS	HIS	E	A	549 - 762	3 - 216
2	1	HIS	HIS	D	B	549 - 762	3 - 216
1	2	LEU	LEU	E	A	549 - 758	3 - 212
2	2	LEU	LEU	B	C	549 - 758	3 - 212
1	3	HIS	HIS	E	A	549 - 760	3 - 214
2	3	HIS	HIS	F	D	549 - 760	3 - 214
1	4	HIS	HIS	E	A	549 - 760	3 - 214
2	4	HIS	HIS	C	E	549 - 760	3 - 214
1	5	LEU	LEU	E	A	549 - 758	3 - 212
2	5	LEU	LEU	A	F	549 - 758	3 - 212
1	6	LEU	LEU	D	B	549 - 758	3 - 212
2	6	LEU	LEU	B	C	549 - 758	3 - 212
1	7	HIS	HIS	D	B	549 - 760	3 - 214
2	7	HIS	HIS	F	D	549 - 760	3 - 214
1	8	HIS	HIS	D	B	549 - 760	3 - 214
2	8	HIS	HIS	C	E	549 - 760	3 - 214
1	9	LEU	LEU	D	B	549 - 758	3 - 212
2	9	LEU	LEU	A	F	549 - 758	3 - 212
1	10	LEU	LEU	B	C	549 - 758	3 - 212
2	10	LEU	LEU	F	D	549 - 758	3 - 212
1	11	LEU	LEU	B	C	549 - 758	3 - 212
2	11	LEU	LEU	C	E	549 - 758	3 - 212
1	12	MET	MET	B	C	549 - 759	3 - 213
2	12	MET	MET	A	F	549 - 759	3 - 213
1	13	HIS	HIS	F	D	549 - 761	3 - 215
2	13	HIS	HIS	C	E	549 - 761	3 - 215
1	14	LEU	LEU	F	D	549 - 758	3 - 212
2	14	LEU	LEU	A	F	549 - 758	3 - 212
1	15	LEU	LEU	C	E	549 - 758	3 - 212
2	15	LEU	LEU	A	F	549 - 758	3 - 212

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	ULP_PROTEASE domain-containing protein Mass: 25190.531 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Orientia tsutsugamushi (bacteria) / Strain: Ikeda / Gene: OTT_1962 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CVM3
#2: Chemical	ChemComp-NI / NICKEL (II) ION / Nickel Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1 / 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 Matthews: 2.93 Å³/Da / Density % sol: 58.04 %
Crystal grow	Temperature: 293 K / Method: microbatch / pH: 7 / Details: 2.4 M sodium malonate pH 7.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.98 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 7, 2019

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.571
1	1	-K, -H, -L	2	0.429

Reflection

Resolution: 2.9→50 Å / Num. obs: 37764 / % possible obs: 100 % / Redundancy: 8.4 % / R_merge(I) obs: 0.116 / R_pim(I) all: 0.042 / R_rim(I) all: 0.123 / Χ²: 1.015 / Net I/σ(I): 4.6 / Num. measured all: 316801

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	Χ²	% possible all
2.9-2.95	6.8	1.948	1863	0.288	0.793	2.107	0.335	100
2.95-3	7.3	1.685	1887	0.372	0.659	1.812	0.341	99.9
3-3.06	7.2	1.4	1897	0.423	0.549	1.506	0.341	99.9
3.06-3.12	8.4	1.229	1879	0.571	0.442	1.308	0.355	100
3.12-3.19	8.9	0.961	1852	0.689	0.336	1.019	0.363	100
3.19-3.27	8.8	0.777	1899	0.734	0.272	0.824	0.386	100
3.27-3.35	8.7	0.591	1889	0.832	0.207	0.627	0.429	100
3.35-3.44	8.8	0.474	1891	0.839	0.167	0.503	0.538	100
3.44-3.54	8.7	0.355	1895	0.927	0.126	0.377	0.595	99.9
3.54-3.65	8.4	0.3	1869	0.931	0.109	0.32	0.796	99.9
3.65-3.78	7.6	0.247	1896	0.949	0.095	0.265	0.972	99.9
3.78-3.94	8.8	0.222	1883	0.955	0.079	0.237	1.226	100
3.94-4.11	9	0.188	1873	0.964	0.066	0.199	1.604	100
4.11-4.33	8.9	0.168	1880	0.976	0.06	0.178	1.871	100
4.33-4.6	8.7	0.154	1901	0.976	0.055	0.164	1.992	100
4.6-4.96	8	0.138	1882	0.978	0.052	0.148	2.075	99.8
4.96-5.46	8.9	0.124	1911	0.984	0.044	0.131	1.742	100
5.46-6.24	9	0.105	1878	0.989	0.037	0.112	1.383	100
6.24-7.86	8.2	0.081	1917	0.994	0.029	0.086	1.371	99.8
7.86-50	8.7	0.057	1922	0.997	0.021	0.061	1.17	99.8

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6X1G

6x1g

Resolution: 2.91→47.86 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.946 / SU B: 16.647 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2082	1904	5 %	RANDOM
R_work	0.1663	-	-	-
obs	0.1683	35812	99.64 %	-

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: 311.16 Å² / B_iso mean: 154.331 Å² / B_iso min: 51.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-19.85 Å²	0 Å²	0 Å²
2-	-	-19.85 Å²	0 Å²
3-	-	-	39.69 Å²

Refinement step

Cycle: final / Resolution: 2.91→47.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10288	0	1	1	10290
B_iso mean	-	-	87.7	51.8	-
Num. residues	-	-	-	-	1279

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	10439
X-RAY DIFFRACTION	r_bond_other_d	0.035	0.017	9882
X-RAY DIFFRACTION	r_angle_refined_deg	1.657	1.632	14019
X-RAY DIFFRACTION	r_angle_other_deg	2.323	1.586	23090
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.731	5	1273
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.149	24.518	571
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.861	15	2077
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.285	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	1345
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	11497
X-RAY DIFFRACTION	r_gen_planes_other	0.015	0.02	1983

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	E	6753	0.12
1	2	D	6753	0.12
2	1	E	6608	0.11
2	2	B	6608	0.11
3	1	E	6574	0.12
3	2	F	6574	0.12
4	1	E	6609	0.11
4	2	C	6609	0.11
5	1	E	6592	0.11
5	2	A	6592	0.11
6	1	D	6615	0.12
6	2	B	6615	0.12
7	1	D	6552	0.13
7	2	F	6552	0.13
8	1	D	6629	0.11
8	2	C	6629	0.11
9	1	D	6636	0.11
9	2	A	6636	0.11
10	1	B	6617	0.12
10	2	F	6617	0.12
11	1	B	6631	0.1
11	2	C	6631	0.1
12	1	B	6716	0.1
12	2	A	6716	0.1
13	1	F	6741	0.11
13	2	C	6741	0.11
14	1	F	6648	0.12
14	2	A	6648	0.12
15	1	C	6718	0.09
15	2	A	6718	0.09

LS refinement shell

Resolution: 2.914→2.989 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.284	113	-
R_work	0.206	2585	-
all	-	2698	-
obs	-	-	95.88 %

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	1.471	0.636	0.19	1.0994	0.6129	0.506	-0.2605	0.0541	-0.0381	-0.0626	0.3667	-0.2112	0.0807	0.0721	-0.1063	0.1535	-0.0618	0.0639	0.3231	-0.0697	0.1567	-19.18	42.62	-39.555
2	1.3797	0.3936	0.0061	0.4937	0.5895	0.941	0.1807	-0.2501	0.1434	0.0055	-0.2455	0.0617	-0.048	-0.2248	0.0648	0.2279	-0.0226	-0.0425	0.2619	-0.0228	0.1073	-31.427	62.421	-6.17
3	1.3278	0.6548	0.0937	0.3364	-0.0473	4.0845	0.2024	0.0547	-0.4206	0.0809	0.0642	-0.2203	-0.5442	0.091	-0.2666	0.4502	-0.0193	-0.0337	0.1396	-0.0958	0.1876	-29.801	74.375	30.678
4	1.08	0.0836	0.8216	0.1464	-0.3188	2.5451	0.1462	0.1168	-0.0193	-0.0409	0.1265	0.1143	0.0887	-0.0336	-0.2727	0.1179	-0.0022	-0.0866	0.2373	0.0711	0.17	-51.719	52.681	-56.639
5	0.1305	0.2589	0.0412	1.7166	-1.0502	3.079	0.1886	0.0204	-0.0616	-0.106	0.4588	0.3906	0.3665	-0.2898	-0.6474	0.48	-0.1019	-0.2549	0.2689	0.2362	0.3072	-33.694	28.145	9.987
6	1.3263	1.9077	-0.4536	3.0097	-1.3397	2.9288	-0.1698	0.1716	-0.2188	-0.4274	0.1929	-0.1473	0.2309	-0.125	-0.0231	0.2637	0.0563	-0.2106	0.184	-0.0725	0.2831	-53.497	59.288	50.145

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	E	549 - 762
2	X-RAY DIFFRACTION	2	D	549 - 761
3	X-RAY DIFFRACTION	3	B	549 - 759
4	X-RAY DIFFRACTION	4	F	549 - 761
5	X-RAY DIFFRACTION	5	C	549 - 761
6	X-RAY DIFFRACTION	6	A	549 - 759

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