PDB-8xfl: The Crystal Structure of MARK4 from Biortus.

ID or keywords:

Entry

Database: PDB / ID: 8xfl

Title

The Crystal Structure of MARK4 from Biortus.

Components

MAP/microtubule affinity-regulating kinase 4

Keywords

TRANSFERASE / Kinase / Cell cycle / Cell division / ATP-binding

Function / homology

Function and homology information

ciliary basal body-plasma membrane docking / protein serine/threonine kinase activity => GO:0004674 / cilium organization / gamma-tubulin complex / positive regulation of protein localization to centrosome / positive regulation of cilium assembly / regulation of centrosome cycle / microtubule bundle formation / gamma-tubulin binding / positive regulation of programmed cell death ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J.

Funding support

1items

Citation

Journal: To Be Published
Title: The Crystal Structure of MARK4 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J.

History

Deposition	Dec 14, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 27, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8xfl.cif.gz	319.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8xfl.ent.gz	203.7 KB	Display	PDB format
PDBx/mmJSON format	8xfl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8xfl_validation.pdf.gz	433.7 KB	Display	wwPDB validaton report
Full document	8xfl_full_validation.pdf.gz	438.4 KB	Display
Data in XML	8xfl_validation.xml.gz	21.5 KB	Display
Data in CIF	8xfl_validation.cif.gz	28.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xf/8xfl ftp://data.pdbj.org/pub/pdb/validation_reports/xf/8xfl	HTTPS FTP

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Related structure data

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

Deposited unit

A: MAP/microtubule affinity-regulating kinase 4

B: MAP/microtubule affinity-regulating kinase 4

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

1

A: MAP/microtubule affinity-regulating kinase 4

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

2

B: MAP/microtubule affinity-regulating kinase 4

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

Unit cell

Length a, b, c (Å)	114.447, 78.103, 86.155
Angle α, β, γ (deg.)	90.000, 122.000, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 51 - 367 / Label seq-ID: 11 - 327

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	MAP/microtubule affinity-regulating kinase 4 Mass: 37562.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MARK4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96L34
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Potassium sodium tartrate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3→48.53 Å / Num. obs: 13003 / % possible obs: 99.9 % / Redundancy: 4.2 % / R_merge(I) obs: 0.074 / Net I/σ(I): 15.1
Reflection shell	Resolution: 3→3.18 Å / R_merge(I) obs: 0.727 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 912

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→41.697 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.912 / SU B: 42 / SU ML: 0.468 / Cross valid method: FREE R-VALUE / ESU R Free: 0.507
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2695	623	4.791 %
R_work	0.2066	12380	-
all	0.21	-	-
obs	-	13003	99.823 %

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 70 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.305 Å²	-0 Å²	1.477 Å²
2-	-	-0.638 Å²	-0 Å²
3-	-	-	-2.534 Å²

Refinement step

Cycle: LAST / Resolution: 3→41.697 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4688	0	0	25	4713

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	4776
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4696
X-RAY DIFFRACTION	r_angle_refined_deg	0.941	1.667	6422
X-RAY DIFFRACTION	r_angle_other_deg	0.325	1.578	10814
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.136	5	570
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.624	5	38
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.203	10	909
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.064	10	221
X-RAY DIFFRACTION	r_chiral_restr	0.045	0.2	713
X-RAY DIFFRACTION	r_chiral_restr_other	0.065	0.2	4
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5497
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1099
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	1048
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	4675
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	2310
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	2605
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	100
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.006	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.125	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.151	0.2	114
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.221	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	3.571	4.898	2301
X-RAY DIFFRACTION	r_mcbond_other	3.571	4.898	2301
X-RAY DIFFRACTION	r_mcangle_it	6.029	8.787	2864
X-RAY DIFFRACTION	r_mcangle_other	6.028	8.787	2865
X-RAY DIFFRACTION	r_scbond_it	3.18	5.207	2475
X-RAY DIFFRACTION	r_scbond_other	3.179	5.208	2476
X-RAY DIFFRACTION	r_scangle_it	5.562	9.462	3558
X-RAY DIFFRACTION	r_scangle_other	5.561	9.462	3559
X-RAY DIFFRACTION	r_lrange_it	11.877	58.519	19254
X-RAY DIFFRACTION	r_lrange_other	11.877	58.519	19255
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.122	0.05	8628

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	0.12215	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.12215	0.05009

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 (%)
3-3.078	0.373	39	0.283	912	X-RAY DIFFRACTION	99.5812
3.078-3.161	0.331	45	0.273	863	X-RAY DIFFRACTION	99.89
3.161-3.253	0.4	41	0.278	862	X-RAY DIFFRACTION	99.779
3.253-3.352	0.399	36	0.278	840	X-RAY DIFFRACTION	99.7722
3.352-3.461	0.261	36	0.26	827	X-RAY DIFFRACTION	99.7688
3.461-3.582	0.362	46	0.275	770	X-RAY DIFFRACTION	100
3.582-3.716	0.258	53	0.232	735	X-RAY DIFFRACTION	99.8733
3.716-3.866	0.308	42	0.241	732	X-RAY DIFFRACTION	99.7423
3.866-4.037	0.251	31	0.216	686	X-RAY DIFFRACTION	100
4.037-4.232	0.355	34	0.214	673	X-RAY DIFFRACTION	100
4.232-4.458	0.258	32	0.177	633	X-RAY DIFFRACTION	100
4.458-4.725	0.255	24	0.16	623	X-RAY DIFFRACTION	100
4.725-5.047	0.225	39	0.153	568	X-RAY DIFFRACTION	100
5.047-5.445	0.289	20	0.192	527	X-RAY DIFFRACTION	100
5.445-5.954	0.317	22	0.195	506	X-RAY DIFFRACTION	100
5.954-6.64	0.39	18	0.227	449	X-RAY DIFFRACTION	99.7863
6.64-7.635	0.193	21	0.183	403	X-RAY DIFFRACTION	100
7.635-9.274	0.18	21	0.168	333	X-RAY DIFFRACTION	99.7183

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	2.9018	-2.6085	1.9067	2.8212	-2.1726	2.087	-0.0577	0.1031	0.3473	0.0825	-0.1981	-0.1719	-0.2042	0.3202	0.2558	0.246	-0.0344	-0.2897	0.6396	0.0036	0.4318	-21.214	-0.179	9.388
2	2.2913	-1.8138	1.9391	2.9706	-2.8615	2.789	0.3587	0.3	-0.3947	-0.2692	-0.0153	0.3074	0.3037	0.0853	-0.3434	0.31	0.037	-0.3818	0.6537	-0.0057	0.4731	-4.306	28.498	29.127

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	51 - 367
2	X-RAY DIFFRACTION	2		B	51 - 367

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