PDB-9rwc: Crystal structure of a sialic acid binding protein, R404A mutant,...

ID or keywords:

Entry

Database: PDB / ID: 9rwc

Title

Crystal structure of a sialic acid binding protein, R404A mutant, from Streptococcus pneumoniae bound to Neu5Ac

Components

Sugar ABC transporter, sugar-binding protein

Keywords

SUGAR BINDING PROTEIN / Sialic acid / Neu5Ac / Periplasmic binding protein / Streptococcus pneumoniae / mutant

Function / homology

maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / N-acetyl-alpha-neuraminic acid / Sugar ABC transporter, sugar-binding protein

Function and homology information

Biological species

Streptococcus pneumoniae TIGR4 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.797 Å

Authors

Atkinson, M. / Lukacik, P. / Strain-Damerell, C.M. / Gloster, T.M. / Walsh, M.A.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published / Year: 2026
Title: Structure of S. pneumoniae sialic acid binding protein; SatA
Authors: Strain-Damerell, C.M. / Atkinson, M. / Meller, C. / Harris, G. / Gloster, T.M. / Lukacik, P. / Walsh, M.A.

History

Deposition	Jul 9, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9rwc.cif.gz	202.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9rwc.ent.gz	150.5 KB	Display	PDB format
PDBx/mmJSON format	9rwc.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/rw/9rwc ftp://data.pdbj.org/pub/pdb/validation_reports/rw/9rwc	HTTPS FTP

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Related structure data

Related structure data	9rsiC 9rslC 9ru4C 9ry2C 9s0lC 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	#113 - May 2009 Influenza Neuraminidase similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (2) #221 - May 2018 Human Papillomavirus and Vaccines similarity (2) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (2) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#113 - May 2009
Influenza Neuraminidase
similarity (1)
#205 - Jan 2017
Nuclear Pore Complex
similarity (2)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (2)
#243 - Mar 2020
Voltage-gated Sodium Channels
similarity (2)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Sugar ABC transporter, sugar-binding protein

B: Sugar ABC transporter, sugar-binding protein

hetero molecules

97.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, peak elution volume corresponds to monomeric mass of chain A or B

Unit cell

Length a, b, c (Å)	78.255, 61.146, 88.873
Angle α, β, γ (deg.)	90.000, 106.127, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 40 - 437 / Label seq-ID: 37 - 434

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein

Sugar ABC transporter, sugar-binding protein

Mass: 48225.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: R404A mutant
Source: (gene. exp.)

Streptococcus pneumoniae TIGR4 (bacteria)
Gene: SP_1683 / Plasmid: pOPINF / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: A0A0H2URD1

#2: Sugar

ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID

Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₉NO₉ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DNeup5Aca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-neuraminic acid	COMMON NAME	GMML 1.0
a-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Chemical

ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1013 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

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: 2.12 Å³/Da / Density % sol: 41.92 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 / Details: 0.1M NaCit, 3.8M ammonium sulfate, pH 5.4

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.9762 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 9, 2025

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9762 Å / Relative weight: 1

Reflection

Resolution: 1.797→85.376 Å / Num. obs: 55625 / % possible obs: 92 % / Redundancy: 7.11 % / CC_1/2: 0.993 / CC_1/2 anomalous: -0.185 / R_merge(I) obs: 0.1722 / R_pim(I) all: 0.0692 / R_rim(I) all: 0.1858 / AbsDiff over sigma anomalous: 0.692 / B_aniso tensor eigenvalue 1: 44.9679 Å² / B_aniso tensor eigenvalue 2: 0 Å² / B_aniso tensor eigenvalue 3: 1.1857 Å² / B_aniso tensor eigenvector 1 ortho1: 0.9959 / B_aniso tensor eigenvector 1 ortho2: 0 / B_aniso tensor eigenvector 1 ortho3: 0.0905 / B_aniso tensor eigenvector 2 ortho1: 0 / B_aniso tensor eigenvector 2 ortho2: 1 / B_aniso tensor eigenvector 2 ortho3: 0 / B_aniso tensor eigenvector 3 ortho1: -0.0905 / B_aniso tensor eigenvector 3 ortho2: 0 / B_aniso tensor eigenvector 3 ortho3: 0.9959 / Aniso diffraction limit 1: 2.449 Å / Aniso diffraction limit 2: 1.636 Å / Aniso diffraction limit 3: 1.668 Å / Aniso diffraction limit axis 1 ortho1: 0.99338 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.1148 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.1148 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.99338 / Net I/σ(I): 7.78 / Num. measured all: 395309 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 92.4 / % possible ellipsoidal: 92 / % possible ellipsoidal anomalous: 92.4 / % possible spherical: 73.8 / % possible spherical anomalous: 74.3 / Redundancy anomalous: 3.63 / Signal type: local

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. measured obs	Num. unique all	Num. unique obs	CC_1/2	CC_1/2 anomalous	R_pim(I) all	R_rim(I) all	AbsDiff over sigma anomalous	% possible anomalous	% possible ellipsoidal	% possible ellipsoidal anomalous	% possible spherical	% possible spherical anomalous	Redundancy anomalous	% possible all
5.472-85.376	6.81	0.0773	14.93	18932	18932	2781	2781	0.996	-0.398	0.0317	0.0837	0.559	100	99.8	100	99.8	100	3.63	99.8
4.318-5.471	7.01	0.0965	14.27	19513	19513	2782	2782	0.994	-0.18	0.0391	0.1043	0.613	100	99.7	100	99.7	100	3.64	99.7
3.767-4.318	7.34	0.0989	14.32	20407	20407	2781	2781	0.994	-0.406	0.0391	0.1064	0.608	100	99.6	100	99.6	100	3.78	99.6
3.416-3.767	7.48	0.095	13.21	20805	20805	2781	2781	0.995	-0.301	0.0373	0.1021	0.593	99.8	99.5	99.8	99.5	99.8	3.84	99.5
3.168-3.416	7.21	0.1115	10.99	20052	20052	2781	2781	0.995	-0.236	0.0446	0.1202	0.646	99.4	99.3	99.4	99.3	99.4	3.7	99.3
2.979-3.168	6.5	0.1391	9	18071	18071	2782	2782	0.992	-0.114	0.0589	0.1513	0.678	99.6	99.3	99.6	99.3	99.6	3.32	99.3
2.825-2.979	6.93	0.1718	8.15	19262	19262	2781	2781	0.989	-0.065	0.0704	0.1858	0.686	98.2	97.3	98.2	97.3	98.2	3.53	97.3
2.693-2.825	7.15	0.2059	7.41	19885	19885	2781	2781	0.987	-0.121	0.0827	0.222	0.694	94.1	92.8	94.1	92.8	94.1	3.63	92.8
2.576-2.692	7.28	0.2181	7.01	20250	20250	2781	2781	0.987	-0.107	0.0867	0.2349	0.708	89	87.5	89	87.5	89	3.69	87.5
2.473-2.576	7.34	0.2311	6.85	20409	20409	2782	2782	0.984	-0.059	0.0915	0.2487	0.706	84.9	83.5	84.9	83.5	84.9	3.71	83.5
2.38-2.473	7.37	0.2538	6.43	20495	20495	2781	2781	0.98	-0.138	0.1	0.273	0.707	81.3	80.2	81.3	78.6	79.9	3.73	80.2
2.295-2.38	7.4	0.2648	6.33	20575	20575	2781	2781	0.98	-0.113	0.104	0.2847	0.718	83.5	82.7	83.5	75.3	76.6	3.74	82.7
2.219-2.295	7.35	0.2761	6.23	20429	20429	2781	2781	0.974	-0.113	0.1091	0.297	0.712	86.2	85.6	86.2	72.3	73.4	3.72	85.6
2.149-2.219	6.88	0.3026	5.65	19134	19134	2782	2782	0.972	-0.14	0.124	0.3273	0.721	87.5	86.9	87.5	68.5	69.7	3.47	86.9
2.083-2.149	6.86	0.3295	5.23	19084	19084	2781	2781	0.97	-0.162	0.1349	0.3563	0.726	90.2	89.7	90.2	65.1	66.1	3.46	89.7
2.022-2.083	7.06	0.3857	4.82	19643	19643	2781	2781	0.948	-0.106	0.1554	0.416	0.744	92.4	92.1	92.4	61.8	62.7	3.57	92.1
1.963-2.022	7.13	0.4332	4.41	19835	19835	2781	2781	0.942	-0.079	0.1736	0.467	0.751	94.2	93.7	94.2	58	58.8	3.6	93.7
1.909-1.963	7.21	0.5115	3.84	20069	20069	2782	2782	0.914	-0.092	0.2036	0.5508	0.739	95.3	94.9	95.3	55.2	55.9	3.64	94.9
1.855-1.909	7.25	0.5685	3.44	20154	20154	2781	2781	0.901	-0.058	0.2256	0.6121	0.754	95	94.9	95	49.2	49.8	3.66	94.9
1.797-1.855	6.58	0.5931	3.02	18305	18305	2781	2781	0.875	-0.048	0.2435	0.6423	0.743	87.2	90.1	87.2	41.1	40.1	3.43	90.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
autoPROC		data reduction
autoPROC		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.797→85.376 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.862 / SU B: 3.449 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.223 / ESU R Free: 0.191
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2525	2715	4.881 %
R_work	0.1947	52910	-
all	0.198	-	-
obs	-	55625	73.814 %

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: 9.143 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.534 Å²	-0 Å²	-0.011 Å²
2-	-	-0.223 Å²	0 Å²
3-	-	-	-0.262 Å²

Refinement step

Cycle: LAST / Resolution: 1.797→85.376 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6248	0	52	1013	7313

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	6590
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6117
X-RAY DIFFRACTION	r_angle_refined_deg	1.548	1.812	8957
X-RAY DIFFRACTION	r_angle_other_deg	0.556	1.775	14224
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.436	5	840
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.707	5	10
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.274	10	1132
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.136	10	299
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	966
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7727
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1445
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1569
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	5866
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	3380
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	3243
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.205	0.2	869
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.016	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.194	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.19	0.2	101
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.181	0.2	77
X-RAY DIFFRACTION	r_mcbond_it	0.833	0.892	3270
X-RAY DIFFRACTION	r_mcbond_other	0.831	0.892	3270
X-RAY DIFFRACTION	r_mcangle_it	1.363	1.594	4107
X-RAY DIFFRACTION	r_mcangle_other	1.363	1.596	4108
X-RAY DIFFRACTION	r_scbond_it	1.416	1.029	3320
X-RAY DIFFRACTION	r_scbond_other	1.412	1.023	3311
X-RAY DIFFRACTION	r_scangle_it	2.318	1.808	4839
X-RAY DIFFRACTION	r_scangle_other	2.316	1.796	4828
X-RAY DIFFRACTION	r_lrange_it	4.312	11.129	8428
X-RAY DIFFRACTION	r_lrange_other	3.962	9.897	8089
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.063	0.05	13827

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	0.06274	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.06274	0.05009

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
1.797-1.844	0.232	108	0.219	2097	0.219	5553	0.964	0.973	39.7083	0.198
1.844-1.894	0.265	129	0.218	2487	0.221	5412	0.954	0.97	48.337	0.198
1.894-1.949	0.253	135	0.189	2629	0.192	5193	0.956	0.975	53.2255	0.164
1.949-2.009	0.249	130	0.18	2822	0.183	5136	0.958	0.977	57.4766	0.155
2.009-2.075	0.251	145	0.187	2861	0.19	4933	0.958	0.976	60.9366	0.163
2.075-2.148	0.267	143	0.178	2972	0.182	4767	0.954	0.978	65.3451	0.152
2.148-2.229	0.244	145	0.181	3047	0.183	4646	0.96	0.977	68.7043	0.154
2.229-2.32	0.237	157	0.17	3083	0.173	4443	0.965	0.98	72.9237	0.147
2.32-2.423	0.231	163	0.177	3108	0.18	4275	0.962	0.979	76.5146	0.153
2.423-2.541	0.241	187	0.176	3131	0.18	4099	0.961	0.978	80.9466	0.152
2.541-2.678	0.285	154	0.206	3232	0.21	3890	0.952	0.97	87.0437	0.182
2.678-2.841	0.225	168	0.183	3237	0.185	3679	0.965	0.977	92.5523	0.159
2.841-3.037	0.25	172	0.197	3217	0.2	3460	0.958	0.974	97.948	0.178
3.037-3.279	0.279	159	0.192	3059	0.196	3245	0.947	0.977	99.1679	0.182
3.279-3.592	0.217	158	0.186	2798	0.187	2981	0.967	0.98	99.1614	0.18
3.592-4.015	0.256	133	0.186	2546	0.189	2690	0.96	0.978	99.5911	0.183
4.015-4.634	0.243	117	0.201	2270	0.203	2396	0.963	0.976	99.6244	0.202
4.634-5.672	0.259	96	0.227	1930	0.229	2035	0.961	0.974	99.5577	0.234
5.672-8.004	0.327	69	0.264	1515	0.266	1588	0.944	0.965	99.7481	0.279
8.004-85.376	0.352	47	0.281	868	0.285	917	0.93	0.954	99.7819	0.341

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Yorodumi