PDB-3hp3: Crystal structure of CXCL12

ID or keywords:

Entry

Database: PDB / ID: 3hp3

Title

Crystal structure of CXCL12

Components

CXCL12 protein

Stromal cell-derived factor 1

Keywords

CYTOKINE /

Chemokine /

CXCL12 / SDF

Function / homology

Function and homology information

chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway /

chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Murphy, J.W. / Lolis, E. / Xiong, Y. / Yuan, H. / Crichlow, G.

Citation

Journal: Proteins / Year: 2009
Title: Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family
Authors: Murphy, J.W. / Yuan, H. / Kong, Y. / Xiong, Y. / Lolis, E.J.

History

Deposition	Jun 3, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 26, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	May 30, 2018	Group: Advisory / Data collection / Derived calculations Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3hp3.cif.gz	139.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3hp3.ent.gz	116.8 KB	Display	PDB format
PDBx/mmJSON format	3hp3.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/hp/3hp3 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hp3	HTTPS FTP

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Related structure data

Related structure data	3gv3C C: citing same article (ref.)
Similar structure data	3oam-2 3jtj-1 4l5g-d 1vic-d 5fzr-d 1wxd-d 7ncc-d 3oam-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3gv3C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (6) #45 - Sep 2003 Estrogen Receptor similarity (2) #107 - Nov 2008 Mechanosensitive Channels similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: CXCL12 protein

B: CXCL12 protein

C: CXCL12 protein

D: CXCL12 protein

E: CXCL12 protein

F: CXCL12 protein

G: CXCL12 protein

H: CXCL12 protein

I: CXCL12 protein

J: CXCL12 protein

hetero molecules

82.2 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CXCL12 protein

B: CXCL12 protein

hetero molecules

defined by author&software
16.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: CXCL12 protein

H: CXCL12 protein

hetero molecules

defined by author&software
16.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: CXCL12 protein

F: CXCL12 protein

hetero molecules

defined by author&software
16.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

E: CXCL12 protein

G: CXCL12 protein

hetero molecules

defined by author&software
16.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: CXCL12 protein

hetero molecules

J: CXCL12 protein

hetero molecules

defined by author&software
16.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	41.834, 117.468, 134.501
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	J
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	C

#1: Protein	CXCL12 protein / Stromal cell-derived factor 1 / Stromal cell-derived factor 1a / cDNA FLJ76575 / highly similar to Homo sapiens chemokine (C-X-C ...Stromal cell-derived factor 1a / cDNA FLJ76575 / highly similar to Homo sapiens chemokine (C-X-C motif) ligand 12 (stromalcell-derived factor 1) (CXCL12) / mRNA / Chemokine (C-X-C motif) ligand 12 (Stromal cell-derived factor 1) / isoform CRA_b Mass: 7980.477 Da / Num. of mol.: 10 / Fragment: UNP residues 22-88 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, hCG_25667 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6ICW0, UniProt: P48061*PLUS
#2: Chemical	ChemComp-AU / GOLD ION Mass: 196.967 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Au
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.07 Å³/Da / Density % sol: 40.6 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl pH 8.5, 20% Jeffamine M-600, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.04 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD
Radiation	Monochromator: Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.04 Å / Relative weight: 1
Reflection	Resolution: 2.2→31 Å / Num. obs: 39406

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Processing

Software

Name	Version	Classification
CBASS		data collection
SHARP		phasing
REFMAC	5.5.0093	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.2→29.18 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.898 / SU B: 18.748 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.245
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27995	709	2.1 %	RANDOM
R_work	0.22832	-	-	-
obs	0.2294	33679	99.63 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 28.569 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.57 Å²	0 Å²	0 Å²
2-	-	0.03 Å²	0 Å²
3-	-	-	0.54 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→29.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4979	0	12	231	5222

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	5094
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.229	1.947	6933
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.086	5	627
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.218	23.965	227
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.248	15	854
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.225	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	802
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	3797
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	6.287	9	3201
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	8.245	9	5150
X-RAY DIFFRACTION	r_scbond_it	8.485	9	1893
X-RAY DIFFRACTION	r_scangle_it	10.726	9	1783
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 408 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	loose positional	0.78	5
B	loose positional	0.84	5
J	loose positional	0.69	5
D	loose positional	0.83	5
E	loose positional	0.69	5
F	loose positional	0.76	5
G	loose positional	1.08	5
H	loose positional	0.86	5
I	loose positional	0.77	5
C	loose positional	0.67	5
A	loose thermal	6.21	10
B	loose thermal	6.37	10
J	loose thermal	5.11	10
D	loose thermal	5.78	10
E	loose thermal	5.95	10
F	loose thermal	6.05	10
G	loose thermal	6.4	10
H	loose thermal	6.48	10
I	loose thermal	5.39	10
C	loose thermal	4.49	10

LS refinement shell

Resolution: 2.2→2.26 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.308	46	-
R_work	0.274	2351	-
obs	-	-	97.36 %

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	8.3145	4.0625	5.1679	2.9623	1.2394	5.8151	0.2836	-0.3749	-0.3619	0.0494	-0.2154	-0.4427	0.362	-0.0304	-0.0682	0.1774	0.0079	-0.0386	0.116	-0.0503	0.1937	6.615	4.432	-49.483
2	5.9629	-0.2609	1.5521	4.3101	1.7836	5.6951	0.057	0.1195	-0.0504	-0.1477	-0.0231	-0.4256	-0.2357	0.399	-0.0339	0.189	-0.0515	-0.0353	0.0581	0.0164	0.0622	7.484	11.954	-45.393
3	1.5186	-1.5408	-0.415	5.9316	-4.3373	5.5932	0.1117	0.0606	0.1246	-0.408	0.0213	-0.0163	0.2384	-0.2028	-0.133	0.1198	-0.0142	-0.0262	0.0456	0.0089	0.0214	-9.45	18.307	-39.946
4	32.693	-1.5693	7.6852	4.1619	-1.9079	3.3406	0.4257	1.0945	-0.0572	-0.362	-0.2671	0.105	-0.1253	0.406	-0.1586	0.2833	-0.075	0.0617	0.2213	-0.1076	0.0865	1.917	22.484	-48.613
5	5.7616	-2.7192	2.5494	7.4357	-4.8318	4.3724	-0.1596	-0.4797	-0.3342	0.4689	0.1894	0.0219	-0.1767	-0.2739	-0.0298	0.1506	-0.0226	0.017	0.0705	0.0223	0.0249	-7.501	7.713	-25.481
6	7.1101	-0.2449	1.7016	9.6293	-0.8863	6.6291	0.1324	-0.2384	-0.3143	0.7062	-0.249	-0.8639	-0.2487	-0.0777	0.1166	0.2012	-0.0485	-0.0613	0.1002	0.09	0.1407	-3.002	2.302	-20.236
7	6.9089	0.9715	-2.8538	1.1019	0.0775	3.9844	-0.4254	0.591	-0.3055	-0.1359	0.2082	-0.1017	0.2241	-0.2003	0.2172	0.2203	-0.0636	0.0339	0.1537	-0.0397	0.0229	2.159	22.835	-14.034
8	55.0431	44.529	-3.5024	31.7929	-1.4602	-3.2229	-0.3814	0.1015	-2.5564	-0.6251	0.1382	-1.9791	0.1493	-0.054	0.2432	1.8825	0.6181	-0.226	1.063	-0.2206	0.8121	8.14	10.946	-21.813
9	5.3965	1.8498	-4.8171	7.2779	-2.6501	8.0669	0.045	0.1113	0.1129	0.0446	0.2047	0.8364	0.2513	-0.3822	-0.2497	0.1046	-0.0007	-0.0099	0.1008	0.0201	0.0999	-11.393	19.487	1.374
10	5.1002	1.9818	-2.6786	7.232	-2.6347	8.8901	-0.3426	-0.3078	-0.5934	-0.0495	-0.1036	-0.1323	0.8515	-0.1017	0.4461	0.1943	0.0183	0.0699	0.0618	0.0281	0.0765	-9.283	13.662	5.261
11	7.2853	-2.813	-3.6257	4.7761	5.6245	6.7596	-0.2045	0.4029	-0.6729	-0.2054	0.3285	-0.2456	-0.1398	0.3852	-0.124	0.1866	-0.0579	0.1086	0.1381	-0.0679	0.2532	7.483	16.574	14.656
12	38.6428	-16.8818	-6.2871	9.1783	0.3157	-1.7021	-0.0782	-0.8584	-0.1092	-2.3812	0.8663	1.0668	1.5172	-0.1517	-0.7881	1.6118	-0.4959	-0.278	0.5571	-0.3696	1.3923	0.18	6.403	4.25
13	5.1957	-2.6813	-3.9012	3.2829	1.4663	8.1015	-0.2619	-0.1471	-0.2101	-0.0129	0.0381	0.0905	0.0311	0.031	0.2238	0.1655	0.0019	-0.0134	0.0093	0.0081	0.0135	-1.99	23.13	30.75
14	3.5358	-2.2758	0.7306	6.0234	-3.3012	6.7003	-0.1929	-0.3096	-0.1829	0.2543	0.2266	0.4434	-0.2435	-0.4003	-0.0337	0.1148	0.0296	0.0031	0.0837	-0.0025	0.0438	-7.137	22.235	37.871
15	4.4752	2.3348	1.5722	7.7943	2.7395	3.1832	-0.2179	0.2549	-0.3542	-0.1778	0.0531	-0.2813	0.026	0.3467	0.1648	0.1367	-0.0086	0.0052	0.0554	0.0281	0.0871	7.418	10.562	45.575
16	10.4202	-1.8798	4.7846	6.0915	-3.7496	7.42	0.1567	0.1869	-0.3178	-0.3014	-0.1347	-0.015	0.3078	0.4667	-0.022	0.1417	-0.0056	0.054	0.0447	-0.0318	0.1234	1.98	5.694	39.098
17	1.1315	-0.2555	-1.4669	7.5055	4.4409	4.3574	0.1579	-0.3426	-0.0923	0.5436	-0.143	-0.2829	-0.0033	0.353	-0.0149	0.228	-0.0838	-0.1128	0.214	0.0549	0.0922	11.46	19.843	60.219
18	5.0633	1.3678	-2.144	5.1315	0.237	3.9868	0.2874	-0.3701	0.0043	0.8057	-0.1373	0.4286	-0.4453	-0.0924	-0.1501	0.3903	-0.0175	0.0517	0.13	0.0488	0.0758	3.745	23.566	62.791
19	3.1619	2.2277	1.1966	2.4952	-2.322	15.664	0.2351	0.2592	0.3931	0.0656	0.1968	0.5949	-0.2978	-0.4137	-0.4319	0.2811	0.0048	-0.0481	0.1393	-0.0086	0.2511	-4.765	7.348	69.431
20	6.2615	-0.8306	-1.9562	5.2572	-2.2865	12.4523	0.1756	0.8198	0.6774	-0.2014	0.5995	0.5069	-0.2292	-1.6417	-0.7751	0.2214	0.0202	-0.0467	0.3898	0.1567	0.1825	-10.112	10.261	62.368

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	I	5 - 23
2	X-RAY DIFFRACTION	2	I	24 - 67
3	X-RAY DIFFRACTION	3	G	3 - 55
4	X-RAY DIFFRACTION	4	G	56 - 67
5	X-RAY DIFFRACTION	5	E	5 - 36
6	X-RAY DIFFRACTION	6	E	37 - 64
7	X-RAY DIFFRACTION	7	B	5 - 60
8	X-RAY DIFFRACTION	8	B	61 - 65
9	X-RAY DIFFRACTION	9	A	4 - 25
10	X-RAY DIFFRACTION	10	A	26 - 65
11	X-RAY DIFFRACTION	11	C	4 - 60
12	X-RAY DIFFRACTION	12	C	61 - 66
13	X-RAY DIFFRACTION	13	H	5 - 41
14	X-RAY DIFFRACTION	14	H	42 - 67
15	X-RAY DIFFRACTION	15	D	4 - 36
16	X-RAY DIFFRACTION	16	D	37 - 67
17	X-RAY DIFFRACTION	17	F	5 - 22
18	X-RAY DIFFRACTION	18	F	23 - 66
19	X-RAY DIFFRACTION	19	J	5 - 42
20	X-RAY DIFFRACTION	20	J	43 - 66

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