PDB-7lda: Crystal structure of a ribose-5-phosphate isomerase from Stenotro...

ID or keywords:

Entry

Database: PDB / ID: 7lda

Title

Crystal structure of a ribose-5-phosphate isomerase from Stenotrophomonas maltophilia K279a

Components

Ribose-5-phosphate isomerase A

Keywords

ISOMERASE / NIAID /

infectious disease / Rpi / RPIA gene /

ribulose-5-phosphate / R5P / Ru5P /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Ribose-5-phosphate isomerase, type A, subgroup / Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) /

ribose-5-phosphate isomerase /

ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / NagB/RpiA transferase-like / Ribose-5-phosphate isomerase A

Function and homology information

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.45 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal structure of a ribose-5-phosphate isomerase from Stenotrophomonas maltophilia K279a
Authors: Edwards, T.E. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease

History

Deposition	Jan 13, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 20, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7lda.cif.gz	198.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7lda.ent.gz	156.7 KB	Display	PDB format
PDBx/mmJSON format	7lda.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/ld/7lda ftp://data.pdbj.org/pub/pdb/validation_reports/ld/7lda	HTTPS FTP

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Related structure data

Related structure data	3enqS S: Starting model for refinement
Similar structure data	2oz1-1 1mxd-d 4edt-d 5oi9-2 4at2-d 1eqn-3 1mow-3 1mwo-d 1mxg-d 5gkk-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
Other databases	TargetTrack: StmaA.00944.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ribose-5-phosphate isomerase A

B: Ribose-5-phosphate isomerase A

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	97.410, 97.410, 129.280
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-544- HOH
2	1	B-600- HOH
3	1	B-746- HOH

#1: Protein	Ribose-5-phosphate isomerase A / Phosphoriboisomerase A / PRI Mass: 24333.932 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: rpiA, Smlt3868 / Production host: Escherichia coli (E. coli) / References: UniProt: B2FT30, ribose-5-phosphate isomerase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 715 / 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: 3.15 Å³/Da / Density % sol: 61 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: StmaA.00944.a.B1.PW38722 at 29.2 mg/mL against MCSG1 screen condition G5: 0.1 M BisTris HCl pH6.5, 2.0M ammonium sulfate supplemented with 25% ethylene glycol as cryo, unique puck ID xqs9-4, 313871g5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.9787 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 27, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.9787 Å / Relative weight: 1

Reflection

Resolution: 1.45→45.58 Å / Num. obs: 110116 / % possible obs: 99.9 % / Redundancy: 9.182 % / B_iso Wilson estimate: 21.692 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.063 / R_rim(I) all: 0.067 / Χ²: 1.041 / Net I/σ(I): 19.16 / Num. measured all: 1011070

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.45-1.49	9.263	0.601	3.62	74493	8042	8042	0.899	0.637	100
1.49-1.53	9.285	0.474	4.57	72877	7849	7849	0.933	0.502	100
1.53-1.57	9.3	0.375	5.88	71175	7653	7653	0.953	0.397	100
1.57-1.62	9.302	0.303	7.21	68882	7405	7405	0.969	0.321	100
1.62-1.67	9.308	0.257	8.36	67028	7201	7201	0.977	0.272	100
1.67-1.73	9.3	0.197	10.66	64786	6966	6966	0.985	0.209	100
1.73-1.8	9.276	0.162	12.89	62542	6742	6742	0.99	0.172	100
1.8-1.87	9.277	0.129	15.95	60066	6475	6475	0.994	0.136	100
1.87-1.96	9.241	0.105	19.23	57580	6231	6231	0.996	0.111	100
1.96-2.05	9.205	0.09	22.43	55117	5988	5988	0.996	0.095	100
2.05-2.16	9.15	0.077	25.7	52011	5684	5684	0.997	0.081	100
2.16-2.29	9.113	0.068	28.82	48938	5370	5370	0.998	0.072	100
2.29-2.45	9.107	0.061	31.14	46465	5102	5102	0.998	0.065	100
2.45-2.65	9.041	0.055	33.62	42871	4743	4742	0.998	0.058	100
2.65-2.9	9.019	0.051	35.89	39478	4381	4377	0.998	0.054	99.9
2.9-3.24	8.984	0.045	38.49	35890	4001	3995	0.999	0.048	99.9
3.24-3.74	8.877	0.039	41.61	31257	3535	3521	0.999	0.042	99.6
3.74-4.59	8.904	0.034	43.18	26898	3035	3021	0.999	0.036	99.5
4.59-6.48	8.928	0.032	42.83	21266	2404	2382	0.999	0.034	99.1
6.48-45.58	8.358	0.029	42.42	11450	1404	1370	0.999	0.031	97.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX	1.19rc4-4035	refinement
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3enq

3enq

Resolution: 1.45→45.58 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1631	2021	1.84 %
R_work	0.1492	108092	-
obs	0.1495	110113	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 53.55 Å² / B_iso mean: 19.289 Å² / B_iso min: 2.42 Å²

Refinement step

Cycle: final / Resolution: 1.45→45.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3257	0	45	730	4032
B_iso mean	-	-	25.64	31.93	-
Num. residues	-	-	-	-	431

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.45-1.49	0.2153	135	0.1915	7627	7762	100
1.49-1.53	0.2101	133	0.177	7640	7773	100
1.53-1.57	0.1812	146	0.1605	7635	7781	100
1.57-1.62	0.1486	158	0.1513	7609	7767	100
1.62-1.68	0.1589	156	0.1478	7637	7793	100
1.68-1.75	0.1618	155	0.1386	7634	7789	100
1.75-1.83	0.158	144	0.1392	7663	7807	100
1.83-1.92	0.1493	143	0.1449	7678	7821	100
1.92-2.04	0.1636	136	0.1437	7703	7839	100
2.04-2.2	0.1487	132	0.1409	7744	7876	100
2.2-2.42	0.147	131	0.1468	7766	7897	100
2.42-2.77	0.1826	133	0.1571	7804	7937	100
2.77-3.49	0.1624	155	0.1493	7844	7999	100
3.49-45.58	0.1621	164	0.1472	8108	8272	99

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	1.3919	0.5909	0.3642	2.5319	-0.1263	1.2884	-0.0262	0.0932	0.0127	-0.1172	-0.0068	-0.0015	-0.0287	0.0746	0.0336	0.0636	-0.0017	-0.0082	0.1187	0.0241	0.0981	-49.0987	31.6009	-22.0899
2	0.6869	-0.3089	0.6805	1.3458	-1.8863	3.7131	-0.072	0.0939	0.1626	0.1057	-0.1046	-0.1061	-0.259	0.3088	0.1825	0.1125	-0.0312	-0.0093	0.1141	0.0226	0.1331	-38.5521	36.831	-10.1068
3	0.5288	-0.017	0.2834	0.9957	0.2882	2.4051	-0.0282	0.054	0.1018	-0.0002	-0.0044	-0.0792	-0.1335	0.2161	0.018	0.0739	-0.0192	-0.0011	0.1189	0.028	0.1181	-40.0904	32.3688	-11.7521
4	0.7874	0.4313	1.7902	8.4706	0.2837	6.6163	0.0541	0.4545	0.4813	-0.4668	-0.0518	0.0346	-0.4854	-0.1667	0.0128	0.1364	0.0106	0.02	0.1838	0.0931	0.2073	-51.5138	41.146	-33.7905
5	8.4012	5.422	2.4531	6.2946	3.1612	5.7825	0.1991	-0.5093	-0.5012	0.7274	-0.2063	-0.0477	0.6015	0.0142	0.0304	0.1995	0.064	0.0209	0.216	0.06	0.1574	-29.8287	5.2078	16.3322
6	3.1421	0.5543	1.2018	4.8293	0.9796	4.5203	-0.1202	-0.1619	0.09	0.2241	0.1221	-0.4398	-0.2711	0.445	-0.0238	0.1336	-0.0152	-0.0091	0.1734	-0.0102	0.1067	-30.8687	19.6207	15.3066
7	5.3334	1.6961	1.5769	7.3007	4.888	8.5016	0.0328	-0.5366	-0.0252	0.6305	-0.0558	-0.2746	0.3521	0.2491	0.0041	0.1439	0.0158	-0.0037	0.1887	0.0359	0.0986	-34.403	12.9508	20.4841
8	6.8742	2.953	-0.0774	4.7448	0.4448	5.2152	0.0559	-0.1312	-0.0701	0.1283	-0.0116	0.0885	-0.0265	-0.0413	-0.0302	0.0663	0.0107	0.0202	0.063	-0.0075	0.0717	-42.3961	18.697	16.0928
9	1.9699	1.1672	-1.0199	3.5767	-3.1746	2.917	0.1776	-0.1427	0.0895	0.3775	-0.0701	0.0626	-0.4236	0.0058	-0.1154	0.1664	-0.0366	-0.009	0.1426	-0.0319	0.0996	-35.8273	27.1758	12.9685
10	0.6979	-0.4074	0.2913	1.0801	0.0381	1.0972	0.0076	-0.0142	-0.0524	0.04	0.011	0.0044	0.0657	0.0629	-0.0213	0.0675	-0.007	0.0098	0.0995	0.0086	0.0772	-34.8718	10.6829	1.0625
11	7.1072	-7.2541	-3.4971	8.3344	3.3465	4.0424	0.2913	0.1558	-0.0319	-0.376	-0.145	0.1061	0.0503	0.0111	-0.0936	0.1083	-0.0041	-0.037	0.1253	0.0109	0.1034	-48.5238	13.3712	-16.1762
12	2.0687	1.0916	1.0764	4.9676	2.7328	3.4928	0.0781	-0.0938	-0.0963	-0.0152	-0.18	0.3188	0.1415	-0.2326	0.1128	0.0691	-0.0056	-0.0084	0.1072	0.0282	0.1057	-51.0207	11.4038	-4.5356
13	3.8197	-1.4571	0.2216	2.9686	0.159	0.4732	-0.005	0.2046	-0.0606	-0.2099	-0.0141	-0.0844	0.0545	0.063	0.0243	0.092	0.0057	-0.0101	0.106	-0.0152	0.0309	-38.2036	10.6	-11.4725
14	9.2035	-1.5502	4.2968	0.8163	-0.9875	2.639	-0.0213	-0.0362	0.0562	-0.0397	-0.0117	-0.0239	-0.062	0.0295	0.0472	0.0888	0.0014	0.012	0.1051	0.0018	0.0809	-35.1969	16.5935	-5.424
15	4.7413	0.4222	1.507	7.0169	-3.0712	4.9925	-0.0781	-0.2313	-0.4618	0.3973	0.0051	-0.5537	0.3152	0.3849	0.1048	0.1865	0.0595	-0.0127	0.1798	0.0194	0.1596	-24.3243	3.4027	9.9613
16	3.8895	0.9957	0.8404	3.0195	4.8268	8.235	-0.0325	0.1911	0.5184	-0.3586	-0.0705	0.3994	-0.624	-0.3377	0.0931	0.1465	0.0297	0.0256	0.1753	0.083	0.1839	-58.4544	41.7668	-29.7132
17	3.0205	0.4733	1.7469	1.9897	0.4194	2.3671	0.0432	-0.0785	-0.0232	0.0576	0.0003	0.07	0.0301	-0.1509	-0.0416	0.0618	-0.0012	0.0155	0.1216	0.0163	0.0997	-64.2372	32.1473	-22.134
18	0.4593	-1.114	0.4297	3.2524	-1.3367	1.608	0.0118	-0.1615	-0.2078	0.0246	0.1268	0.3113	0.1192	-0.1406	-0.1303	0.0926	-0.0358	-0.037	0.1605	0.0259	0.1568	-62.339	21.1592	-19.4251

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 76 through 115 )	B	76 - 115
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 116 through 149 )	B	116 - 149
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 150 through 203 )	B	150 - 203
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 204 through 215 )	B	204 - 215
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1 through 15 )	A	1 - 15
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 16 through 27 )	A	16 - 27
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 28 through 43 )	A	28 - 43
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 44 through 61 )	A	44 - 61
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 62 through 75 )	A	62 - 75
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 76 through 134 )	A	76 - 134
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 135 through 149 )	A	135 - 149
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 150 through 165 )	A	150 - 165
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 166 through 187 )	A	166 - 187
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 188 through 203 )	A	188 - 203
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 204 through 215 )	A	204 - 215
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 0 through 15 )	B	0 - 15
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 16 through 61 )	B	16 - 61
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 62 through 75 )	B	62 - 75

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