PDB-7oxx: CrabP2 mutant R30AK31A

ID or keywords:

Entry

Database: PDB / ID: 7oxx

Title

CrabP2 mutant R30AK31A

Components

Cellular retinoic acid-binding protein 2

Keywords

TRANSPORT PROTEIN / retinoic acid / CRABP2 / cyclin / CDK4/6 / nuclear hormone receptor / signalling kinase

Function / homology

Function and homology information

positive regulation of collateral sprouting / retinoid binding / retinoic acid binding / retinal binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.33 Å

Authors

Tomlinson, C.W.E. / Basle, A. / Pohl, E.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Structural requirements for the specific binding of CRABP2 to cyclin D3
Authors: Pastok, M.W. / Tomlinson, C.W.E. / Tatum, N.J. / Basle, A. / Noble, M.E.M. / Pohl, E. / Endicott, J.A.

History

Deposition	Jun 23, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7oxx.cif.gz	426.8 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	7oxx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7oxx_validation.pdf.gz	444.4 KB	Display	wwPDB validaton report
Full document	7oxx_full_validation.pdf.gz	448.5 KB	Display
Data in XML	7oxx_validation.xml.gz	25.6 KB	Display
Data in CIF	7oxx_validation.cif.gz	37.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ox/7oxx ftp://data.pdbj.org/pub/pdb/validation_reports/ox/7oxx	HTTPS FTP

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Related structure data

Related structure data	7oxwC 2frsS 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
Related items in Molecule of the Month	#236 - Aug 2019 Cyclin and Cyclin-dependent Kinase similarity (1) #193 - Jan 2016 Siderocalin similarity (3) #155 - Nov 2012 Vitamin D Receptor similarity (1) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Cellular retinoic acid-binding protein 2

B: Cellular retinoic acid-binding protein 2

C: Cellular retinoic acid-binding protein 2

D: Cellular retinoic acid-binding protein 2

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	51.170, 106.020, 55.540
Angle α, β, γ (deg.)	90.000, 101.700, 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	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ASN	ASN	ARG	ARG	A	A	3 - 137	3 - 137
2	2	1	ASN	ASN	ARG	ARG	B	B	3 - 137	3 - 137
3	3	2	ASN	ASN	ARG	ARG	A	A	3 - 137	3 - 137
4	4	2	ASN	ASN	ARG	ARG	C	C	3 - 137	3 - 137
5	5	3	ASN	ASN	ARG	ARG	A	A	3 - 137	3 - 137
6	6	3	ASN	ASN	ARG	ARG	D	D	3 - 137	3 - 137
7	7	4	PRO	PRO	ARG	ARG	B	B	2 - 137	2 - 137
8	8	4	PRO	PRO	ARG	ARG	C	C	2 - 137	2 - 137
9	9	5	PRO	PRO	ARG	ARG	B	B	2 - 137	2 - 137
10	10	5	PRO	PRO	ARG	ARG	D	D	2 - 137	2 - 137
11	11	6	MET	MET	GLU	GLU	C	C	1 - 138	1 - 138
12	12	6	MET	MET	GLU	GLU	D	D	1 - 138	1 - 138

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	Cellular retinoic acid-binding protein 2 / Cellular retinoic acid-binding protein II / CRABP-II Mass: 15568.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29373
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 2.37 Å³/Da / Density % sol: 48.08 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 150 mM MgCl2, 100 mM Bis-Tris pH 6.5 and 25% PEG 3350.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9686 Å / Relative weight: 1
Reflection	Resolution: 1.33→54.39 Å / Num. obs: 128510 / % possible obs: 97.1 % / Redundancy: 3.3 % / CC_1/2: 0.996 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.33→1.35 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6247 / CC_1/2: 0.411 / % possible all: 94.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
XDS		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building
MolProbity		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2FRS

2frs

Resolution: 1.33→54.386 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.963 / SU B: 3.376 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1996	6503	5.062 %
R_work	0.1584	121967	-
all	0.161	-	-
obs	-	128470	96.888 %

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: 25.357 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.599 Å²	0 Å²	1.37 Å²
2-	-	-3.617 Å²	0 Å²
3-	-	-	-0.506 Å²

Refinement step

Cycle: LAST / Resolution: 1.33→54.386 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4333	0	4	399	4736

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	4532
X-RAY DIFFRACTION	r_bond_other_d	0.012	0.017	4438
X-RAY DIFFRACTION	r_angle_refined_deg	1.859	1.651	6158
X-RAY DIFFRACTION	r_angle_other_deg	1.587	1.581	10284
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.925	5	589
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.942	23.604	222
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.808	15	877
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.026	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	623
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	5087
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	975
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	634
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	4053
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	2088
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	2300
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	269
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.036	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.339	0.2	12
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.113	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.141	0.2	26
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.168	0.2	25
X-RAY DIFFRACTION	r_mcbond_it	2.699	2.235	2239
X-RAY DIFFRACTION	r_mcbond_other	2.557	2.233	2238
X-RAY DIFFRACTION	r_mcangle_it	3.218	3.374	2804
X-RAY DIFFRACTION	r_mcangle_other	3.236	3.376	2805
X-RAY DIFFRACTION	r_scbond_it	4.135	2.814	2293
X-RAY DIFFRACTION	r_scbond_other	4.107	2.81	2290
X-RAY DIFFRACTION	r_scangle_it	4.997	4.003	3333
X-RAY DIFFRACTION	r_scangle_other	4.985	4.001	3332
X-RAY DIFFRACTION	r_lrange_it	4.598	26.514	4807
X-RAY DIFFRACTION	r_lrange_other	4.524	26.184	4735
X-RAY DIFFRACTION	r_rigid_bond_restr	8.602	3	8970
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.079	0.05	3929
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.104	0.05	3850
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.111	0.05	3830
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.108	0.05	3842
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.113	0.05	3802
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.099	0.05	3865

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	0.07891	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07891	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.10446	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.10446	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11127	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.11127	0.05008
4	7	B	X-RAY DIFFRACTION	Local ncs	0.10846	0.05008
4	8	C	X-RAY DIFFRACTION	Local ncs	0.10846	0.05008
5	9	B	X-RAY DIFFRACTION	Local ncs	0.11306	0.05008
5	10	D	X-RAY DIFFRACTION	Local ncs	0.11306	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.09864	0.05008
6	12	D	X-RAY DIFFRACTION	Local ncs	0.09864	0.05008

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
1.33-1.365	0.322	488	0.292	8818	0.294	9786	0.789	0.839	95.095	0.278
1.365-1.402	0.308	433	0.269	8708	0.271	9530	0.84	0.866	95.9182	0.248
1.402-1.443	0.275	435	0.237	8523	0.238	9283	0.874	0.899	96.499	0.214
1.443-1.487	0.236	427	0.206	8213	0.207	8978	0.898	0.915	96.2352	0.181
1.487-1.536	0.242	435	0.175	8001	0.178	8783	0.92	0.941	96.0492	0.152
1.536-1.589	0.195	436	0.16	7674	0.162	8441	0.947	0.953	96.0787	0.14
1.589-1.649	0.203	384	0.143	7537	0.146	8152	0.949	0.962	97.1663	0.126
1.649-1.717	0.196	372	0.121	7263	0.124	7806	0.952	0.976	97.8094	0.109
1.717-1.793	0.191	364	0.132	6989	0.135	7551	0.959	0.968	97.3778	0.124
1.793-1.88	0.181	366	0.122	6614	0.125	7179	0.948	0.97	97.228	0.119
1.88-1.982	0.184	330	0.124	6346	0.127	6872	0.955	0.972	97.1478	0.127
1.982-2.102	0.19	296	0.144	5981	0.146	6453	0.95	0.961	97.2726	0.153
2.102-2.247	0.18	270	0.139	5699	0.141	6115	0.953	0.963	97.6124	0.153
2.247-2.427	0.186	281	0.143	5253	0.145	5675	0.953	0.96	97.5154	0.164
2.427-2.658	0.197	258	0.144	4841	0.147	5222	0.952	0.965	97.6446	0.17
2.658-2.97	0.186	273	0.151	4323	0.153	4720	0.952	0.961	97.3729	0.181
2.97-3.428	0.213	246	0.168	3869	0.171	4202	0.943	0.957	97.9296	0.206
3.428-4.195	0.177	169	0.161	3312	0.162	3544	0.962	0.963	98.2223	0.199
4.195-5.914	0.198	151	0.167	2564	0.168	2752	0.965	0.969	98.6555	0.221
5.914-54.386	0.223	89	0.201	1440	0.202	1553	0.953	0.952	98.4546	0.268

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