PDB-9fgp: cilia and flagella associated protein 299

ID or keywords:

Entry

Database: PDB / ID: 9fgp

Title

cilia and flagella associated protein 299

Components

Cilia- and flagella-associated protein 299

Keywords

UNKNOWN FUNCTION / Soluble / Ageing / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Protein of unknown function DUF4464 / Domain of unknown function (DUF4464) / nucleus / cytoplasm / Cilia- and flagella-associated protein 299

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.49 Å

Authors

Wright, N.D. / Koekemoer, L. / Structural Genomics Consortium (SGC)

Funding support

1items

Citation

Journal: To Be Published
Title: cilia and flagella associated protein 299
Authors: Wright, N.D. / Koekemoer, L. / Williams, E. / Wang, S. / Bradshaw, W.J. / Teare, H. / Gao, Q. / Balcomb, B.H. / Duman, R. / Winter, G. / Keegan, R. / Isupov, M. / Lebedev, A. / Marsden, B. / von Delft, F.

History

Deposition	May 24, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 12, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9fgp.cif.gz	80.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9fgp.ent.gz	56.7 KB	Display	PDB format
PDBx/mmJSON format	9fgp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9fgp_validation.pdf.gz	429.8 KB	Display	wwPDB validaton report
Full document	9fgp_full_validation.pdf.gz	432.6 KB	Display
Data in XML	9fgp_validation.xml.gz	15.6 KB	Display
Data in CIF	9fgp_validation.cif.gz	22.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fg/9fgp ftp://data.pdbj.org/pub/pdb/validation_reports/fg/9fgp	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: Cilia- and flagella-associated protein 299

B: Cilia- and flagella-associated protein 299

hetero molecules

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

1

A: Cilia- and flagella-associated protein 299

hetero molecules

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

2

B: Cilia- and flagella-associated protein 299

hetero molecules

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

Unit cell

Length a, b, c (Å)	31.756, 34.449, 58.984
Angle α, β, γ (deg.)	91.354, 100.003, 90.09
Int Tables number	1
Space group name H-M	P1

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: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 90 - 229 / Label seq-ID: 1 - 140

Dom-ID
1
2

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

#1: Protein	Cilia- and flagella-associated protein 299 Mass: 16169.093 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CFAP299, C4orf22 / Plasmid: pRARE2 Details (production host): pRARE2 plasmid encoding rare codon tRNAs Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6V702
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 264 / 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: 1.96 Å³/Da / Density % sol: 37.39 % / Description: CFAP299A-p003
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20% PEG6000 -- 10% ethylene glycol -- 0.1M MES pH 6.0 -- 0.01M zinc chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 5, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.49→58.071 Å / Num. obs: 28810 / % possible obs: 71.6 % / Redundancy: 3.5 % / B_iso Wilson estimate: 8.45 Å² / CC_1/2: 0.998 / Net I/σ(I): 1.29
Reflection shell	Resolution: 1.49→1.52 Å / Num. unique obs: 53 / CC_1/2: 0.925

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
xia2		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.49→58.071 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.931 / SU B: 1.522 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.115 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2189	1450	5.033 %
R_work	0.1745	27359	-
all	0.177	-	-
obs	-	28809	71.625 %

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: 13.565 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.357 Å²	0.219 Å²	-0.03 Å²
2-	-	-0.22 Å²	0.395 Å²
3-	-	-	0.534 Å²

Refinement step

Cycle: LAST / Resolution: 1.49→58.071 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2279	0	12	264	2555

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	2391
X-RAY DIFFRACTION	r_angle_refined_deg	1.962	1.821	3247
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.4	5	294
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.775	5	22
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.235	10	416
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.583	10	125
X-RAY DIFFRACTION	r_chiral_restr	0.131	0.2	353
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1850
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	1056
X-RAY DIFFRACTION	r_nbtor_refined	0.317	0.2	1613
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	205
X-RAY DIFFRACTION	r_metal_ion_refined	0.061	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.183	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.182	0.2	31
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.091	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.361	1.102	1152
X-RAY DIFFRACTION	r_mcangle_it	2.186	1.967	1448
X-RAY DIFFRACTION	r_scbond_it	2.113	1.291	1239
X-RAY DIFFRACTION	r_scangle_it	3.179	2.265	1797
X-RAY DIFFRACTION	r_lrange_it	5.058	17.131	3793
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.074	0.05	4814

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	0.07424	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07424	0.0501

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
1.49-1.529	0.312	19	0.25	194	0.256	2943	0.947	0.96	7.2375	0.232
1.529-1.571	0.222	28	0.186	530	0.187	2940	0.969	0.98	18.9796	0.163
1.571-1.616	0.191	36	0.202	770	0.202	2790	0.982	0.977	28.8889	0.172
1.616-1.666	0.218	58	0.189	1091	0.19	2761	0.971	0.979	41.6154	0.158
1.666-1.72	0.247	83	0.193	1368	0.197	2653	0.966	0.977	54.6928	0.165
1.72-1.781	0.27	86	0.174	1608	0.179	2561	0.962	0.982	66.146	0.149
1.781-1.848	0.216	102	0.169	1858	0.171	2462	0.974	0.982	79.6101	0.145
1.848-1.923	0.191	126	0.162	2146	0.164	2387	0.974	0.984	95.1822	0.141
1.923-2.009	0.221	100	0.166	2181	0.168	2291	0.972	0.983	99.5635	0.148
2.009-2.106	0.246	117	0.168	2070	0.172	2187	0.963	0.983	100	0.154
2.106-2.22	0.226	96	0.171	1976	0.173	2072	0.971	0.983	100	0.157
2.22-2.355	0.217	90	0.165	1890	0.168	1980	0.975	0.983	100	0.153
2.355-2.517	0.215	78	0.18	1744	0.182	1822	0.971	0.98	100	0.166
2.517-2.718	0.187	91	0.176	1646	0.177	1737	0.979	0.981	100	0.164
2.718-2.977	0.245	93	0.179	1482	0.183	1575	0.96	0.98	100	0.169
2.977-3.327	0.186	53	0.178	1379	0.178	1432	0.976	0.981	100	0.174
3.327-3.84	0.186	55	0.163	1213	0.164	1268	0.979	0.985	100	0.162
3.84-4.698	0.17	76	0.157	1001	0.158	1077	0.985	0.986	100	0.161
4.698-6.622	0.297	37	0.193	782	0.197	819	0.973	0.982	100	0.199
6.622-58.071	0.423	26	0.246	430	0.255	456	0.951	0.969	100	0.265

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