PDB-27aa: Crystal structure of the complex of short peptidoglycan recogniti...

ID or keywords:

Entry

Database: PDB / ID: 27aa

Title

Crystal structure of the complex of short peptidoglycan recognition protein from Camelus dromedarius with nonanoic acid at 1.83 A resolution

Components

Peptidoglycan recognition protein 1

Keywords

IMMUNE SYSTEM / Short Peptidoglycan Recognition Protein / PGRP-S / Camelus dromedarius

Function / homology

Function and homology information

peptidoglycan immune receptor activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / negative regulation of cytokine production / detection of bacterium / peptidoglycan catabolic process / defense response to Gram-positive bacterium / innate immune response / extracellular region / zinc ion binding
Similarity search - Function

Biological species

Camelus dromedarius (Arabian camel)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.834 Å

Authors

Barik, D. / Ahmad, N. / Singh, P.K. / Yadav, S.P. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the complex of short peptidoglycan recognition protein from Camelus dromedarius with nonanoic acid at 1.83 A resolution
Authors: Barik, D. / Ahmad, N. / Singh, P.K. / Yadav, S.P. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.

History

Deposition	May 22, 2026	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Jun 17, 2026	ID: 5DWF
Revision 1.0	Jun 17, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	27aa.cif.gz	153.6 KB	Display	PDBx/mmCIF format
PDB format	pdb27aa.ent.gz	116.1 KB	Display	PDB format
PDBx/mmJSON format	27aa.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/7a/27aa ftp://data.pdbj.org/pub/pdb/validation_reports/7a/27aa	HTTPS FTP

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Related structure data

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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Peptidoglycan recognition protein 1

B: Peptidoglycan recognition protein 1

C: Peptidoglycan recognition protein 1

D: Peptidoglycan recognition protein 1

hetero molecules

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

1

A: Peptidoglycan recognition protein 1

hetero molecules

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

2

B: Peptidoglycan recognition protein 1

hetero molecules

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

3

C: Peptidoglycan recognition protein 1

hetero molecules

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

4

D: Peptidoglycan recognition protein 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	88.775, 101.525, 163.087
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	C-357- HOH
2	1	D-349- HOH
3	1	D-356- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
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: CYS / Beg label comp-ID: CYS / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 6 - 171 / Label seq-ID: 1 - 166

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	A	A
2	1	1	B	B
3	2	2	A	A
4	2	2	C	C
5	3	3	A	A
6	3	3	D	D
7	4	4	B	B
8	4	4	C	C
9	5	5	B	B
10	5	5	D	D
11	6	6	C	C
12	6	6	D	D

NCS ensembles :

ID	Details (eV)
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

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Peptidoglycan recognition protein 1 / Peptidoglycan recognition protein short / PGRP-S Mass: 18501.947 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Camelus dromedarius (Arabian camel) / References: UniProt: Q9GK12

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Non-polymers , 5 types, 300 molecules

#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Chemical	ChemComp-KNA / nonanoic acid Mass: 158.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₉H₁₈O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	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: 2.48 Å³/Da / Density % sol: 50.46 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350 Sodium potassium tartarate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.99 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Nov 14, 2014
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 1.83→50 Å / Num. obs: 64628 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / R_sym value: 0.06 / Net I/av σ(I): 16.4 / Net I/σ(I): 2
Reflection shell	Resolution: 1.83→1.86 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1288 / R_sym value: 0.43

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
HKL-2000		data collection
SCALEPACK		data scaling
autoPROC		data processing
PDB_EXTRACT		data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.834→34.256 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.908 / SU B: 8.476 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.176
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3211	1288	1.993 %
R_work	0.272	63339	-
all	0.273	-	-
obs	-	64627	99.751 %

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: 32.334 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.218 Å²	0 Å²	0 Å²
2-	-	-2.616 Å²	-0 Å²
3-	-	-	0.397 Å²

Refinement step

Cycle: LAST / Resolution: 1.834→34.256 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5203	0	53	293	5549

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	5410
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4953
X-RAY DIFFRACTION	r_angle_refined_deg	1.436	1.802	7363
X-RAY DIFFRACTION	r_angle_other_deg	0.515	1.754	11315
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.82	5	662
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.059	5	64
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.237	10	805
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.298	10	261
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	764
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6737
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1399
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	1201
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.208	0.2	5052
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	2688
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	2818
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.22	0.2	287
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.066	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.261	0.2	45
X-RAY DIFFRACTION	r_nbd_other	0.238	0.2	87
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.188	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.847	3.218	2654
X-RAY DIFFRACTION	r_mcbond_other	2.847	3.218	2654
X-RAY DIFFRACTION	r_mcangle_it	4.275	5.765	3311
X-RAY DIFFRACTION	r_mcangle_other	4.275	5.766	3312
X-RAY DIFFRACTION	r_scbond_it	3.334	3.583	2756
X-RAY DIFFRACTION	r_scbond_other	3.334	3.583	2757
X-RAY DIFFRACTION	r_scangle_it	5.165	6.422	4051
X-RAY DIFFRACTION	r_scangle_other	5.165	6.422	4052
X-RAY DIFFRACTION	r_lrange_it	7.814	39.954	25691
X-RAY DIFFRACTION	r_lrange_other	7.808	39.954	25680
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.102	0.05	5537
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.096	0.05	5608
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.104	0.05	5556
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.09	0.05	5526
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.103	0.05	5466
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.086	0.05	5617

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	0.10153	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10153	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09581	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09581	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10407	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.10407	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.09043	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.09043	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.10273	0.0501
5	10	D	X-RAY DIFFRACTION	Local ncs	0.10273	0.0501
6	11	C	X-RAY DIFFRACTION	Local ncs	0.08604	0.0501
6	12	D	X-RAY DIFFRACTION	Local ncs	0.08604	0.0501

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
1.834-1.881	0.47	102	0.435	4515	0.436	4747	0.766	0.821	97.2614	0.428
1.881-1.933	0.417	97	0.432	4515	0.432	4612	0.856	0.84	100	0.421
1.933-1.989	0.476	88	0.408	4388	0.409	4476	0.814	0.863	100	0.392
1.989-2.05	0.421	98	0.416	4250	0.416	4348	0.855	0.859	100	0.397
2.05-2.116	0.444	86	0.404	4192	0.405	4278	0.838	0.863	100	0.382
2.116-2.19	0.439	78	0.392	3972	0.393	4050	0.834	0.879	100	0.365
2.19-2.273	0.41	71	0.368	3877	0.369	3948	0.875	0.895	100	0.335
2.273-2.365	0.41	81	0.347	3729	0.348	3810	0.891	0.91	100	0.31
2.365-2.47	0.386	65	0.318	3603	0.319	3668	0.889	0.926	100	0.283
2.47-2.59	0.382	62	0.308	3453	0.309	3515	0.909	0.933	100	0.273
2.59-2.729	0.354	66	0.308	3256	0.309	3322	0.914	0.933	100	0.268
2.729-2.893	0.356	65	0.289	3102	0.291	3167	0.916	0.944	100	0.259
2.893-3.091	0.314	71	0.257	2920	0.258	2991	0.939	0.957	100	0.235
3.091-3.337	0.268	53	0.23	2713	0.231	2766	0.956	0.965	100	0.219
3.337-3.652	0.248	49	0.209	2552	0.209	2601	0.963	0.972	100	0.205
3.652-4.077	0.244	57	0.19	2278	0.191	2335	0.96	0.977	100	0.195
4.077-4.697	0.17	33	0.156	2040	0.156	2073	0.985	0.985	100	0.169
4.697-5.726	0.18	29	0.173	1746	0.173	1775	0.987	0.984	100	0.188
5.726-7.986	0.298	25	0.183	1393	0.185	1418	0.971	0.981	100	0.201
7.986-34.256	0.212	12	0.18	845	0.18	873	0.973	0.975	98.1672	0.205

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