PDB-7z5h: human Zn MATCAP

ID or keywords:

Entry

Database: PDB / ID: 7z5h

Title

human Zn 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 /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Bak, J. / Adamopoulos, 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
Revision 1.2	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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	7z5h.cif.gz	967.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7z5h.ent.gz	795.4 KB	Display	PDB format
PDBx/mmJSON format	7z5h.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/z5/7z5h ftp://data.pdbj.org/pub/pdb/validation_reports/z5/7z5h	HTTPS FTP

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Related structure data

Related structure data	14529C 7z5gSC 7z6sC S: Starting model for refinement 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

hetero molecules

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

1

A: Uncharacterized protein KIAA0895-like

hetero molecules

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

2

B: Uncharacterized protein KIAA0895-like

hetero molecules

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

3

C: Uncharacterized protein KIAA0895-like

hetero molecules

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

4

D: Uncharacterized protein KIAA0895-like

hetero molecules

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

Unit cell

Length a, b, c (Å)	55.646, 88.067, 165.581
Angle α, β, γ (deg.)	90.000, 90.767, 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:

Beg auth comp-ID: VAL / Beg label comp-ID: VAL

Dom-ID	Component-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	1	LEU	LEU	A	A	141 - 469	5 - 333
2	2	1	LEU	LEU	B	B	141 - 469	5 - 333
3	3	2	LEU	LEU	A	A	141 - 469	5 - 333
4	4	2	LEU	LEU	C	C	141 - 469	5 - 333
5	5	3	PRO	PRO	A	A	141 - 470	5 - 334
6	6	3	PRO	PRO	D	D	141 - 470	5 - 334
7	7	4	PRO	PRO	B	B	141 - 470	5 - 334
8	8	4	PRO	PRO	C	C	141 - 470	5 - 334
9	9	5	LEU	LEU	B	B	141 - 469	5 - 333
10	10	5	LEU	LEU	D	D	141 - 469	5 - 333
11	11	6	LEU	LEU	C	C	141 - 469	5 - 333
12	12	6	LEU	LEU	D	D	141 - 469	5 - 333

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: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES-NaOH, 4.3M NaCl, 2 uM ZnCl2, 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: 1.28096 Å

Detector

Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 20, 2020

Radiation

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

Radiation wavelength

Wavelength: 1.28096 Å / Relative weight: 1

Reflection

Resolution: 2.5→47.083 Å / Num. obs: 55542 / % possible obs: 100 % / Redundancy: 6.8 % / CC_1/2: 0.996 / R_merge(I) obs: 0.173 / R_pim(I) all: 0.108 / R_rim(I) all: 0.204 / Net I/σ(I): 9.1

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
10.61-47.04	6.5	0.03	773	0.999	0.019	0.036
2.5-2.57	7	1.727	4531	0.56	1.073	2.038

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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:

MOLECULAR REPLACEMENT
Starting model: 7Z5G

7z5g

Resolution: 2.5→47.083 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.925 / WR_factor R_free: 0.213 / WR_factor R_work: 0.189 / SU B: 31.337 / SU ML: 0.302 / Average fsc free: 0.8345 / Average fsc work: 0.8422 / Cross valid method: FREE R-VALUE / ESU R: 0.663 / ESU R Free: 0.296
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.255	2762	4.974 %
R_work	0.2319	52763	-
all	0.233	-	-
obs	-	55525	99.914 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 59.829 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.711 Å²	0 Å²	0.921 Å²
2-	-	0.234 Å²	-0 Å²
3-	-	-	-0.969 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→47.083 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10848	0	4	161	11013

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.018	11108
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	10403
X-RAY DIFFRACTION	r_angle_refined_deg	0.978	1.876	15037
X-RAY DIFFRACTION	r_angle_other_deg	0.964	2.938	23797
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.747	5	1319
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.13	22.795	594
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.914	15	1904
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.768	15	120
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	1592
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	12693
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2859
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	2277
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.159	0.2	10021
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	5374
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	6673
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	241
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.226	0.2	53
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	167
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.106	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.284	3.008	5288
X-RAY DIFFRACTION	r_mcbond_other	1.284	3.008	5287
X-RAY DIFFRACTION	r_mcangle_it	2.225	4.508	6603
X-RAY DIFFRACTION	r_mcangle_other	2.225	4.508	6604
X-RAY DIFFRACTION	r_scbond_it	1.241	3.107	5820
X-RAY DIFFRACTION	r_scbond_other	1.241	3.106	5817
X-RAY DIFFRACTION	r_scangle_it	2.148	4.617	8434
X-RAY DIFFRACTION	r_scangle_other	2.148	4.617	8433
X-RAY DIFFRACTION	r_lrange_it	4.182	34.537	12504
X-RAY DIFFRACTION	r_lrange_other	4.18	34.529	12498
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.083	0.05	11125
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.074	0.05	11041
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.075	0.05	11111
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.083	0.05	11123
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.082	0.05	11133
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.061	0.05	11293

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	0.08303	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08303	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07422	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.07422	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07501	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.07501	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.08252	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.08252	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.08156	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.08156	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.06099	0.05009
6	12	D	X-RAY DIFFRACTION	Local ncs	0.06099	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 (%)
2.5-2.565	0.402	207	0.385	3863	X-RAY DIFFRACTION	99.8283
2.565-2.635	0.359	171	0.361	3837	X-RAY DIFFRACTION	99.9252
2.635-2.711	0.312	191	0.353	3651	X-RAY DIFFRACTION	99.948
2.711-2.795	0.325	239	0.328	3533	X-RAY DIFFRACTION	100
2.795-2.887	0.33	181	0.31	3481	X-RAY DIFFRACTION	99.9727
2.887-2.988	0.3	170	0.292	3329	X-RAY DIFFRACTION	100
2.988-3.101	0.33	157	0.279	3284	X-RAY DIFFRACTION	100
3.101-3.227	0.321	177	0.27	3082	X-RAY DIFFRACTION	100
3.227-3.371	0.328	126	0.251	3039	X-RAY DIFFRACTION	100
3.371-3.535	0.274	145	0.229	2866	X-RAY DIFFRACTION	100
3.535-3.726	0.211	128	0.206	2762	X-RAY DIFFRACTION	100
3.726-3.952	0.208	128	0.191	2577	X-RAY DIFFRACTION	100
3.952-4.225	0.197	125	0.179	2427	X-RAY DIFFRACTION	99.9217
4.225-4.563	0.19	120	0.168	2249	X-RAY DIFFRACTION	99.9578
4.563-4.998	0.206	108	0.164	2096	X-RAY DIFFRACTION	100
4.998-5.587	0.231	109	0.181	1887	X-RAY DIFFRACTION	99.9499
5.587-6.451	0.214	113	0.204	1637	X-RAY DIFFRACTION	99.8858
6.451-7.897	0.191	79	0.169	1431	X-RAY DIFFRACTION	99.9338
7.897-11.156	0.211	63	0.161	1105	X-RAY DIFFRACTION	100
11.156-47.083	0.169	25	0.2	628	X-RAY DIFFRACTION	98.3434

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	1.5519	0.8203	0.0228	1.729	0.4411	1.8262	-0.0433	0.2454	-0.1164	0.0179	0.0264	-0.1821	0.2916	0.2049	0.017	0.3675	0.0453	0.2015	0.0802	0.0091	0.1378	-25.2284	-1.9615	-21.1562
2	1.2908	-0.4609	0.855	1.7301	-0.4598	3.96	-0.1028	0.1904	-0.1722	-0.1833	0.3051	0.3158	-0.3354	0.1242	-0.2023	0.5244	-0.2271	0.2332	0.2782	-0.0501	0.2009	-3.3918	-0.4759	-60.2173
3	2.6301	-0.9067	-0.1283	0.8556	-0.5752	1.9518	-0.1888	0.1627	-0.0114	-0.1198	0.1546	-0.0464	-0.1515	0.1002	0.0342	0.4756	-0.2055	0.2375	0.1946	-0.046	0.1624	-9.2678	42.0796	-63.2142
4	1.6428	0.8523	-0.6086	1.4973	-0.0759	3.1267	0.0318	0.0965	0.1316	-0.0036	0.0212	-0.0199	-0.1952	-0.0671	-0.0529	0.2061	0.0265	0.1364	0.0092	0.0254	0.1095	-17.2388	40.6978	-22.0234

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	141 - 470
3	X-RAY DIFFRACTION	3	ALL	C	141 - 470
4	X-RAY DIFFRACTION	4	ALL	D	141 - 471

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