PDB-7z5g: human apo MATCAP

ID or keywords:

Entry

Database: PDB / ID: 7z5g

Title

human apo MATCAP

Components

Uncharacterized protein KIAA0895-like

Keywords

PEPTIDE BINDING PROTEIN /

detyrosination / microtubule-binding / zinc-metalloprotease / tyrosine carboxypeptidase

Function / homology

Function and homology information

tubulinyl-Tyr carboxypeptidase /

tubulin-tyrosine carboxypeptidase /

metallocarboxypeptidase activity /

brain development /

microtubule /

proteolysis /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.113 Å

Authors

Bak, J. / Adamoupolos, A. / Heidebrecht, T. / Perrakis, A.

Funding support

Netherlands, 1items

Citation

Journal: Science / Year: 2022
Title: Posttranslational modification of microtubules by the MATCAP detyrosinase.
Authors: Lisa Landskron / Jitske Bak / Athanassios Adamopoulos / Konstantina Kaplani / Maria Moraiti / Lisa G van den Hengel / Ji-Ying Song / Onno B Bleijerveld / Joppe Nieuwenhuis / Tatjana ...
Abstract: The detyrosination-tyrosination cycle involves the removal and religation of the C-terminal tyrosine of α-tubulin and is implicated in cognitive, cardiac, and mitotic defects. The vasohibin-small ...

History

Deposition	Mar 9, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 11, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 1, 2022	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7z5g.cif.gz	966.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7z5g.ent.gz	814.9 KB	Display	PDB format
PDBx/mmJSON format	7z5g.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/z5/7z5g ftp://data.pdbj.org/pub/pdb/validation_reports/z5/7z5g	HTTPS FTP

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Related structure data

Related structure data	14529C 7z5hC 7z6sC 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

Deposited unit

A: Uncharacterized protein KIAA0895-like

B: Uncharacterized protein KIAA0895-like

C: Uncharacterized protein KIAA0895-like

D: Uncharacterized protein KIAA0895-like

156 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein KIAA0895-like

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

2

B: Uncharacterized protein KIAA0895-like

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

3

C: Uncharacterized protein KIAA0895-like

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

4

D: Uncharacterized protein KIAA0895-like

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

Unit cell

Length a, b, c (Å)	55.852, 88.028, 165.613
Angle α, β, γ (deg.)	90.000, 90.676, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	140 - 469
2	2	1	B	140 - 469
3	3	2	A	141 - 469
4	4	2	C	141 - 469
5	5	3	A	141 - 470
6	6	3	D	141 - 470
7	7	4	B	141 - 469
8	8	4	C	141 - 469
9	9	5	B	141 - 469
10	10	5	D	141 - 469
11	11	6	C	141 - 469
12	12	6	D	141 - 469

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
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Uncharacterized protein KIAA0895-like Mass: 39001.453 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0895L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q68EN5
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.61 Å³/Da / Density % sol: 52.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES-NaOH, 4.3M NaCl, 5 mM EDTA pH 7

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 0.999997 Å

Detector

Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 4, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.999997 Å / Relative weight: 1

Reflection

Resolution: 2.11→47.203 Å / Num. obs: 90835 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC_1/2: 0.994 / R_merge(I) obs: 0.063 / R_pim(I) all: 0.062 / R_rim(I) all: 0.088 / Net I/σ(I): 9.5

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
11.57-47.16	3.1	0.024	1812	0.959	0.024	0.034
2.11-2.15	3.2	0.712	13906	0.665	0.708	1.004

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building
MolProbity		model building

Refinement

Method to determine structure:

SIRAS / Resolution: 2.113→47.203 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.944 / WR_factor R_free: 0.239 / WR_factor R_work: 0.204 / SU B: 20.854 / SU ML: 0.229 / Average fsc free: 0.7905 / Average fsc work: 0.7989 / Cross valid method: FREE R-VALUE / ESU R: 0.24 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2506	4578	5.041 %
R_work	0.2171	86245	-
all	0.219	-	-
obs	-	90823	98.692 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 57.995 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.685 Å²	0 Å²	3.76 Å²
2-	-	-1.067 Å²	-0 Å²
3-	-	-	-2.706 Å²

Refinement step

Cycle: LAST / Resolution: 2.113→47.203 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10856	0	0	202	11058

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.018	11116
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	10414
X-RAY DIFFRACTION	r_angle_refined_deg	1.46	1.877	15048
X-RAY DIFFRACTION	r_angle_other_deg	1.126	2.938	23822
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.433	5	1320
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.724	22.795	594
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.19	15	1906
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.679	15	120
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1594
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	12700
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2860
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	2232
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.173	0.2	9704
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	5450
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	7011
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	262
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.08	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.271	0.2	47
X-RAY DIFFRACTION	r_nbd_other	0.231	0.2	183
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.129	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	2.808	2.736	5292
X-RAY DIFFRACTION	r_mcbond_other	2.807	2.736	5291
X-RAY DIFFRACTION	r_mcangle_it	4.232	4.097	6608
X-RAY DIFFRACTION	r_mcangle_other	4.233	4.098	6609
X-RAY DIFFRACTION	r_scbond_it	3.594	3.061	5824
X-RAY DIFFRACTION	r_scbond_other	3.593	3.06	5821
X-RAY DIFFRACTION	r_scangle_it	5.404	4.471	8440
X-RAY DIFFRACTION	r_scangle_other	5.403	4.471	8439
X-RAY DIFFRACTION	r_lrange_it	7.436	31.899	12518
X-RAY DIFFRACTION	r_lrange_other	7.432	31.868	12504
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.083	0.05	11128
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.096	0.05	10943
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.093	0.05	10979
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.088	0.05	11117
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.087	0.05	11061
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.08	0.05	11207

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	0.08306	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08306	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09594	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09594	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09283	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.09283	0.05008
4	7	B	X-RAY DIFFRACTION	Local ncs	0.08838	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.08838	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.08654	0.05008
5	10	D	X-RAY DIFFRACTION	Local ncs	0.08654	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.08041	0.05009
6	12	D	X-RAY DIFFRACTION	Local ncs	0.08041	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 (%)
2.113-2.168	0.407	325	0.382	6234	X-RAY DIFFRACTION	96.6122
2.168-2.227	0.34	316	0.346	6255	X-RAY DIFFRACTION	99.2448
2.227-2.292	0.331	331	0.333	6021	X-RAY DIFFRACTION	99.4676
2.292-2.362	0.306	335	0.3	5916	X-RAY DIFFRACTION	99.4907
2.362-2.44	0.319	328	0.285	5684	X-RAY DIFFRACTION	99.4048
2.44-2.525	0.301	294	0.268	5531	X-RAY DIFFRACTION	99.4876
2.525-2.621	0.322	309	0.254	5275	X-RAY DIFFRACTION	99.6965
2.621-2.728	0.303	255	0.253	5195	X-RAY DIFFRACTION	99.8534
2.728-2.849	0.287	225	0.252	4981	X-RAY DIFFRACTION	99.7318
2.849-2.988	0.286	218	0.24	4743	X-RAY DIFFRACTION	99.7788
2.988-3.15	0.275	262	0.22	4500	X-RAY DIFFRACTION	99.7069
3.15-3.341	0.296	231	0.225	4234	X-RAY DIFFRACTION	99.5541
3.341-3.571	0.256	153	0.205	4032	X-RAY DIFFRACTION	98.8427
3.571-3.857	0.212	218	0.181	3623	X-RAY DIFFRACTION	96.8971
3.857-4.225	0.199	212	0.168	3231	X-RAY DIFFRACTION	95.3212
4.225-4.723	0.209	159	0.159	3022	X-RAY DIFFRACTION	95.8132
4.723-5.453	0.175	145	0.164	2667	X-RAY DIFFRACTION	96.999
5.453-6.677	0.218	118	0.173	2309	X-RAY DIFFRACTION	98.2193
6.677-9.435	0.169	80	0.14	1806	X-RAY DIFFRACTION	96.9666
9.435-47.203	0.174	64	0.177	986	X-RAY DIFFRACTION	96.5961

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	1.4697	0.6524	-0.0082	1.585	0.296	1.6846	-0.1424	0.2035	-0.1835	-0.0323	0.0524	-0.1494	0.4357	0.1637	0.0899	0.1381	0.005	0.0039	0.1573	0.0429	0.1957	-25.4108	-1.8317	-21.15
2	1.5294	-0.439	0.9443	1.3742	-0.5025	3.5344	-0.0674	0.185	-0.2257	-0.1678	0.3015	0.25	-0.3183	0.1705	-0.2341	0.463	-0.3026	0.0681	0.3849	-0.1071	0.3044	-3.7975	-0.3982	-60.22
3	2.6666	-0.673	-0.176	0.5692	-0.4592	1.8636	-0.2342	0.2348	-0.0163	-0.0756	0.2005	-0.0383	-0.2289	0.095	0.0337	0.2226	-0.2531	0.0261	0.3438	-0.0986	0.2385	-9.2446	41.9304	-63.1989
4	1.6431	0.5859	-0.7207	1.1052	0.0793	3.2235	0.0094	0.0617	0.1845	-0.0341	0.0793	-0.0128	-0.2911	-0.0247	-0.0887	0.0373	-0.0027	-0.0327	0.089	0.0054	0.165	-17.2172	40.6734	-22.0293

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	140 - 471
2	X-RAY DIFFRACTION	2	ALL	B	140 - 470
3	X-RAY DIFFRACTION	3	ALL	C	141 - 470
4	X-RAY DIFFRACTION	4	ALL	D	141 - 471

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