PDB-7oxw: CrabP2 mutant R30DK31D

ID or keywords:

Entry

Database: PDB / ID: 7oxw

Title

CrabP2 mutant R30DK31D

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 /

retinal binding /

retinoic acid 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: 1.16 Å

Authors

Pastok, M.W. / Basle, A. / Endicott, J.A.

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 / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7oxw.cif.gz	123.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7oxw.ent.gz	93.4 KB	Display	PDB format
PDBx/mmJSON format	7oxw.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/ox/7oxw ftp://data.pdbj.org/pub/pdb/validation_reports/ox/7oxw	HTTPS FTP

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Related structure data

Related structure data	7oxxC 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

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	45.300, 92.290, 98.760
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

#1: Protein	Cellular retinoic acid-binding protein 2 / Cellular retinoic acid-binding protein II / CRABP-II Mass: 16068.256 Da / Num. of mol.: 1 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-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.3 Å³/Da / Density % sol: 62.77 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 100 mM Sodium acetate pH 4.5 and 2.0 M ammonium sulfate

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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 PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.16→46.15 Å / Num. obs: 71395 / % possible obs: 99.4 % / Redundancy: 6.4 % / CC_1/2: 0.999 / Net I/σ(I): 19.4
Reflection shell	Resolution: 1.16→1.18 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3221 / CC_1/2: 0.946 / % possible all: 91.8

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Processing

Software

Name	Version	Classification
XDS		data reduction
xia2		data reduction
Aimless		data scaling
MolProbity		model building
Coot		model building
PHASER		phasing
REFMAC	5	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2FRS

2frs

Resolution: 1.16→46.145 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.967 / SU B: 0.906 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1737	3459	4.845 %
R_work	0.1624	67935	-
all	0.163	-	-
obs	-	71394	99.321 %

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: 18.576 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.006 Å²	-0 Å²	-0 Å²
2-	-	1.239 Å²	0 Å²
3-	-	-	-1.233 Å²

Refinement step

Cycle: LAST / Resolution: 1.16→46.145 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1124	0	24	157	1305

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	1202
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1137
X-RAY DIFFRACTION	r_angle_refined_deg	1.72	1.652	1638
X-RAY DIFFRACTION	r_angle_other_deg	1.516	1.582	2645
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.464	5	156
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.697	24.237	59
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.06	15	226
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.387	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	162
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1348
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	248
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	173
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	999
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	527
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	629
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.201	0.2	92
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.285	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.202	0.2	33
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.123	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	1.411	1.609	589
X-RAY DIFFRACTION	r_mcbond_other	1.405	1.605	587
X-RAY DIFFRACTION	r_mcangle_it	1.685	2.427	738
X-RAY DIFFRACTION	r_mcangle_other	1.687	2.428	739
X-RAY DIFFRACTION	r_scbond_it	2.692	2.003	613
X-RAY DIFFRACTION	r_scbond_other	2.432	1.982	598
X-RAY DIFFRACTION	r_scangle_it	3.445	2.876	894
X-RAY DIFFRACTION	r_scangle_other	2.892	2.826	871
X-RAY DIFFRACTION	r_lrange_it	2.956	20.104	1258
X-RAY DIFFRACTION	r_lrange_other	2.832	19.462	1227
X-RAY DIFFRACTION	r_rigid_bond_restr	2.225	3	2335

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
1.16-1.19	0.256	226	0.253	4676	0.253	5283	0.748	0.73	92.7882	0.211
1.19-1.223	0.218	251	0.216	4801	0.216	5116	0.859	0.862	98.749	0.175
1.223-1.258	0.224	206	0.183	4764	0.185	4974	0.89	0.914	99.9196	0.15
1.258-1.297	0.165	244	0.152	4623	0.153	4871	0.95	0.951	99.9179	0.124
1.297-1.339	0.17	228	0.143	4438	0.144	4669	0.957	0.959	99.9357	0.119
1.339-1.386	0.16	242	0.128	4313	0.13	4557	0.962	0.968	99.9561	0.109
1.386-1.439	0.143	209	0.113	4169	0.114	4379	0.972	0.977	99.9772	0.097
1.439-1.497	0.164	228	0.112	4034	0.114	4263	0.966	0.977	99.9765	0.1
1.497-1.564	0.141	172	0.112	3878	0.114	4051	0.974	0.979	99.9753	0.105
1.564-1.64	0.128	215	0.114	3665	0.115	3881	0.979	0.981	99.9742	0.109
1.64-1.729	0.152	182	0.121	3539	0.123	3721	0.975	0.978	100	0.119
1.729-1.833	0.133	180	0.121	3353	0.121	3533	0.979	0.979	100	0.125
1.833-1.96	0.144	152	0.135	3142	0.136	3295	0.974	0.975	99.9697	0.146
1.96-2.116	0.158	144	0.143	2941	0.144	3085	0.976	0.976	100	0.159
2.116-2.318	0.154	130	0.147	2728	0.147	2858	0.971	0.972	100	0.172
2.318-2.591	0.171	138	0.158	2454	0.159	2593	0.966	0.967	99.9614	0.191
2.591-2.99	0.194	99	0.189	2214	0.189	2315	0.951	0.956	99.9136	0.233
2.99-3.658	0.201	104	0.184	1849	0.185	1957	0.95	0.959	99.7956	0.233
3.658-5.157	0.205	68	0.174	1488	0.175	1559	0.968	0.969	99.8076	0.24
5.157-46.145	0.201	41	0.286	866	0.282	920	0.938	0.933	98.587	0.377

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