PDB-2hzr: Crystal structure of human apolipoprotein D (ApoD)

ID or keywords:

Entry

Database: PDB / ID: 2hzr

Title

Crystal structure of human apolipoprotein D (ApoD)

Components

Apolipoprotein D

Keywords

TRANSPORT PROTEIN / lipocalin / beta barrel / bilin-binding protein

Function / homology

Function and homology information

negative regulation of lipoprotein lipid oxidation / Transport of fatty acids / negative regulation of T cell migration / negative regulation of smooth muscle cell-matrix adhesion / peripheral nervous system axon regeneration / negative regulation of focal adhesion assembly / lipid transporter activity / tissue regeneration / negative regulation of monocyte chemotactic protein-1 production / negative regulation of platelet-derived growth factor receptor signaling pathway ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Eichinger, A. / Skerra, A.

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: Structural insight into the dual ligand specificity and mode of high density lipoprotein association of apolipoprotein d.
Authors: Eichinger, A. / Nasreen, A. / Kim, H.J. / Skerra, A.

History

Deposition	Aug 9, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 14, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3	Nov 20, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2hzr.cif.gz	51.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2hzr.ent.gz	34.5 KB	Display	PDB format
PDBx/mmJSON format	2hzr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2hzr_validation.pdf.gz	428.1 KB	Display	wwPDB validaton report
Full document	2hzr_full_validation.pdf.gz	429.1 KB	Display
Data in XML	2hzr_validation.xml.gz	9.6 KB	Display
Data in CIF	2hzr_validation.cif.gz	13.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hz/2hzr ftp://data.pdbj.org/pub/pdb/validation_reports/hz/2hzr	HTTPS FTP

-
Related structure data

Related structure data	2hzqC C: citing same article (ref.)
Similar structure data	5qha-d 3bnw-2 1mac-2 5ypk-8 5dvh-d 2r0x-d 2d37-d 5cit-2 2hzq-d 6mdu-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (5) #155 - Nov 2012 Vitamin D Receptor similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Apolipoprotein D

20 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)	49.247, 49.247, 143.486
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Apolipoprotein D / Apo-D / ApoD Mass: 19988.102 Da / Num. of mol.: 1 / Mutation: L23P, W99H, C116S, I118S, L120S, P133V, N134A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APOD / Plasmid: pApoD27delta(QA) / Production host: Escherichia coli (E. coli) / Strain (production host): KS272 / References: UniProt: P05090
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 43.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.1 M lithium sulfate, 0.1 M ammonium formate, 0.075 M Hepes/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-4 / Wavelength: 0.97940,0.97969,0.96863

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2005 / Details: mirrors

Radiation

Monochromator: Si 111 DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9794	1
2	0.97969	1
3	0.96863	1

Reflection

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	R_sym value	D res high (Å)	D res low (Å)	Num. obs	% possible obs
15	1	6.4	254351	0.067	0.067	1.8	46.58	17002	99.1
13.4	2	8.1	169962	0.06	0.06	2	46.727	12649	99.4
13.2	3	7.9	112336	0.073	0.073	2.3	46.742	8486	99.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
5.69	49.27	95.2	1	0.051	0.051	12
4.02	5.69	99.8	1	0.05	0.05	13.8
3.29	4.02	99.8	1	0.052	0.052	14.5
2.85	3.29	99.6	1	0.059	0.059	14.9
2.55	2.85	99.5	1	0.068	0.068	15.2
2.32	2.55	99.4	1	0.079	0.079	15.3
2.15	2.32	99.2	1	0.094	0.094	15.4
2.01	2.15	99.1	1	0.119	0.119	15.4
1.9	2.01	98.9	1	0.19	0.19	15.6
1.8	1.9	98.7	1	0.285	0.285	14.7
6.32	49.39	94.4	2	0.038	0.038	10.4
4.47	6.32	99.8	2	0.04	0.04	12.4
3.65	4.47	99.9	2	0.043	0.043	12.9
3.16	3.65	99.9	2	0.046	0.046	13.3
2.83	3.16	99.7	2	0.058	0.058	13.5
2.58	2.83	99.6	2	0.075	0.075	13.6
2.39	2.58	99.5	2	0.104	0.104	13.7
2.24	2.39	99.4	2	0.136	0.136	13.8
2.11	2.24	99.2	2	0.168	0.168	13.9
2	2.11	99.2	2	0.228	0.228	13.9
7.27	49.39	97.7	3	0.046	0.046	10.2
5.14	7.27	99.7	3	0.042	0.042	12.1
4.2	5.14	99.9	3	0.042	0.042	12.6
3.64	4.2	99.9	3	0.048	0.048	13.1
3.25	3.64	99.7	3	0.059	0.059	13.3
2.97	3.25	99.6	3	0.088	0.088	13.5
2.75	2.97	99.6	3	0.119	0.119	13.6
2.57	2.75	99.6	3	0.195	0.195	13.6
2.42	2.57	99.3	3	0.291	0.291	13.7
2.3	2.42	99.5	3	0.36	0.36	13.8

Reflection

Resolution: 1.8→46.58 Å / Num. all: 17219 / Num. obs: 17002 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 15 % / R_merge(I) obs: 0.067 / R_sym value: 0.067 / Net I/σ(I): 6.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.8-1.9	14.7	0.285	2.2	35742	2437	0.285	98.7
1.9-2.01	15.6	0.19	3	35080	2252	0.19	98.9
2.01-2.15	15.4	0.119	6	33540	2172	0.119	99.1
2.15-2.32	15.4	0.094	7.3	31360	2035	0.094	99.2
2.32-2.55	15.3	0.079	8.7	28515	1861	0.079	99.4
2.55-2.85	15.2	0.068	4.3	26036	1715	0.068	99.5
2.85-3.29	14.9	0.059	10.3	23208	1555	0.059	99.6
3.29-4.02	14.5	0.052	11	19068	1312	0.052	99.8
4.02-5.69	13.8	0.05	11.7	14608	1061	0.05	99.8
5.69-49.27	12	0.051	12	7194	602	0.051	95.2

-
Phasing

Phasing

Method:

MAD

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	1.8	29	13911	2889
ISO_2	0.217	0.193	1.8	29	10086	2233
ISO_3	0.35	0.375	1.8	29	6515	1746
ANO_1	0.714	0	1.8	29	13891	0
ANO_2	0.925	0	1.8	29	10084	0
ANO_3	0.964	0	1.8	29	6516	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Reflection acentric	Reflection centric
ISO_1	7.77-29	0	0	112	118
ISO_1	5.6-7.77	0	0	248	141
ISO_1	4.6-5.6	0	0	327	140
ISO_1	3.99-4.6	0	0	411	147
ISO_1	3.58-3.99	0	0	480	146
ISO_1	3.27-3.58	0	0	525	153
ISO_1	3.03-3.27	0	0	578	140
ISO_1	2.84-3.03	0	0	642	151
ISO_1	2.68-2.84	0	0	669	139
ISO_1	2.54-2.68	0	0	722	152
ISO_1	2.42-2.54	0	0	768	152
ISO_1	2.32-2.42	0	0	781	136
ISO_1	2.23-2.32	0	0	832	151
ISO_1	2.15-2.23	0	0	876	146
ISO_1	2.08-2.15	0	0	904	144
ISO_1	2.01-2.08	0	0	949	156
ISO_1	1.95-2.01	0	0	973	138
ISO_1	1.9-1.95	0	0	990	141
ISO_1	1.85-1.9	0	0	1056	148
ISO_1	1.8-1.85	0	0	1068	150
ANO_1	7.77-29	0.611	0	111	0
ANO_1	5.6-7.77	0.577	0	248	0
ANO_1	4.6-5.6	0.611	0	327	0
ANO_1	3.99-4.6	0.652	0	411	0
ANO_1	3.58-3.99	0.635	0	480	0
ANO_1	3.27-3.58	0.662	0	525	0
ANO_1	3.03-3.27	0.679	0	578	0
ANO_1	2.84-3.03	0.652	0	642	0
ANO_1	2.68-2.84	0.665	0	669	0
ANO_1	2.54-2.68	0.679	0	722	0
ANO_1	2.42-2.54	0.699	0	767	0
ANO_1	2.32-2.42	0.728	0	780	0
ANO_1	2.23-2.32	0.756	0	832	0
ANO_1	2.15-2.23	0.779	0	875	0
ANO_1	2.08-2.15	0.811	0	903	0
ANO_1	2.01-2.08	0.843	0	948	0
ANO_1	1.95-2.01	0.861	0	973	0
ANO_1	1.9-1.95	0.903	0	987	0
ANO_1	1.85-1.9	0.954	0	1055	0
ANO_1	1.8-1.85	0.969	0	1058	0
ISO_2	7.77-29	0.154	0.155	111	115
ISO_2	5.6-7.77	0.075	0.081	248	140
ISO_2	4.6-5.6	0.092	0.082	327	136
ISO_2	3.99-4.6	0.092	0.097	411	140
ISO_2	3.58-3.99	0.086	0.093	480	139
ISO_2	3.27-3.58	0.087	0.114	525	146
ISO_2	3.03-3.27	0.1	0.092	578	132
ISO_2	2.84-3.03	0.118	0.14	642	143
ISO_2	2.68-2.84	0.157	0.175	669	133
ISO_2	2.54-2.68	0.19	0.244	722	142
ISO_2	2.42-2.54	0.23	0.277	768	145
ISO_2	2.32-2.42	0.262	0.292	781	128
ISO_2	2.23-2.32	0.33	0.419	832	141
ISO_2	2.15-2.23	0.379	0.448	876	137
ISO_2	2.08-2.15	0.421	0.49	904	135
ISO_2	2.01-2.08	0.515	0.551	949	147
ISO_2	1.95-2.01	0.53	0.526	263	34
ISO_2	1.9-1.95	0	0	0	0
ISO_2	1.85-1.9	0	0	0	0
ISO_2	1.8-1.85	0	0	0	0
ANO_2	7.77-29	0.559	0	109	0
ANO_2	5.6-7.77	0.519	0	248	0
ANO_2	4.6-5.6	0.697	0	327	0
ANO_2	3.99-4.6	0.771	0	411	0
ANO_2	3.58-3.99	0.795	0	480	0
ANO_2	3.27-3.58	0.818	0	525	0
ANO_2	3.03-3.27	0.876	0	578	0
ANO_2	2.84-3.03	0.86	0	642	0
ANO_2	2.68-2.84	0.872	0	669	0
ANO_2	2.54-2.68	0.917	0	722	0
ANO_2	2.42-2.54	0.963	0	767	0
ANO_2	2.32-2.42	0.95	0	782	0
ANO_2	2.23-2.32	0.972	0	832	0
ANO_2	2.15-2.23	0.975	0	877	0
ANO_2	2.08-2.15	0.986	0	904	0
ANO_2	2.01-2.08	0.986	0	948	0
ANO_2	1.95-2.01	0.986	0	263	0
ANO_2	1.9-1.95	0	0	0	0
ANO_2	1.85-1.9	0	0	0	0
ANO_2	1.8-1.85	0	0	0	0
ISO_3	7.77-29	0.454	0.601	112	117
ISO_3	5.6-7.77	0.294	0.312	248	140
ISO_3	4.6-5.6	0.254	0.265	327	139
ISO_3	3.99-4.6	0.229	0.244	411	144
ISO_3	3.58-3.99	0.24	0.239	480	145
ISO_3	3.27-3.58	0.245	0.265	525	151
ISO_3	3.03-3.27	0.262	0.255	578	138
ISO_3	2.84-3.03	0.314	0.316	642	149
ISO_3	2.68-2.84	0.383	0.426	669	137
ISO_3	2.54-2.68	0.458	0.482	722	150
ISO_3	2.42-2.54	0.536	0.587	768	151
ISO_3	2.32-2.42	0.583	0.647	780	134
ISO_3	2.23-2.32	0.649	0.741	253	51
ISO_3	2.15-2.23	0	0	0	0
ISO_3	2.08-2.15	0	0	0	0
ISO_3	2.01-2.08	0	0	0	0
ISO_3	1.95-2.01	0	0	0	0
ISO_3	1.9-1.95	0	0	0	0
ISO_3	1.85-1.9	0	0	0	0
ISO_3	1.8-1.85	0	0	0	0
ANO_3	7.77-29	0.813	0	114	0
ANO_3	5.6-7.77	0.788	0	248	0
ANO_3	4.6-5.6	0.825	0	327	0
ANO_3	3.99-4.6	0.866	0	411	0
ANO_3	3.58-3.99	0.896	0	480	0
ANO_3	3.27-3.58	0.916	0	525	0
ANO_3	3.03-3.27	0.955	0	578	0
ANO_3	2.84-3.03	0.959	0	642	0
ANO_3	2.68-2.84	0.978	0	669	0
ANO_3	2.54-2.68	0.988	0	722	0
ANO_3	2.42-2.54	0.992	0	767	0
ANO_3	2.32-2.42	0.993	0	780	0
ANO_3	2.23-2.32	0.999	0	253	0
ANO_3	2.15-2.23	0	0	0	0
ANO_3	2.08-2.15	0	0	0	0
ANO_3	2.01-2.08	0	0	0	0
ANO_3	1.95-2.01	0	0	0	0
ANO_3	1.9-1.95	0	0	0	0
ANO_3	1.85-1.9	0	0	0	0
ANO_3	1.8-1.85	0	0	0	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	46.506	20.391	81.773	SE	20.43	1.11
2	39.834	3.892	86.024	SE	4.97	0.29
3	35.486	-4.468	75.152	SE	30.53	0.68

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
SHARP		phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
ADSC	Quantum	data collection
MOSFLM		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.8→30 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.924 / SU B: 2.64 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.137 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25	864	5.1 %	RANDOM
R_work	0.202	-	-	-
all	0.205	17219	-	-
obs	0.205	16987	98.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 22.818 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.78 Å²	0 Å²	0 Å²
2-	-	0.78 Å²	0 Å²
3-	-	-	-1.55 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1283	0	0	152	1435

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	1316
X-RAY DIFFRACTION	r_angle_refined_deg	1.431	1.941	1793
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.13	5	158
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.702	25.5	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.398	15	220
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.116	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	201
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	998
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	561
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	908
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	118
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.209	0.2	38
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.167	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	1.185	1.5	834
X-RAY DIFFRACTION	r_mcangle_it	1.806	2	1322
X-RAY DIFFRACTION	r_scbond_it	2.987	3	556
X-RAY DIFFRACTION	r_scangle_it	4.474	4.5	471

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	65	-
R_work	0.215	1157	-
obs	-	1222	98.15 %

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi