PDB-3qd5: Crystal structure of a putative ribose-5-phosphate isomerase from...

ID or keywords:

Entry

Database: PDB / ID: 3qd5

Title

Crystal structure of a putative ribose-5-phosphate isomerase from Coccidioides immitis solved by combined iodide ion SAD and MR

Components

putative ribose-5-phosphate isomerase

Keywords

ISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Coccidioidomycosis / putative uncharacterized protein / hypothetical protein / ribose-5-phosphate isomerase / iodide ion

Function / homology

Function and homology information

Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds / isomerase activity / carbohydrate metabolic process
Similarity search - Function

Biological species

Coccidioides immitis (fungus)

Method

X-RAY DIFFRACTION /

SAD,

MOLECULAR REPLACEMENT /

SAD /

molecular replacement / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Bmc Struct.Biol. / Year: 2011
Title: Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis.
Authors: Edwards, T.E. / Abramov, A.B. / Smith, E.R. / Baydo, R.O. / Leonard, J.T. / Leibly, D.J. / Thompkins, K.B. / Clifton, M.C. / Gardberg, A.S. / Staker, B.L. / Van Voorhis, W.C. / Myler, P.J. / Stewart, L.J.

History

Deposition	Jan 17, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 26, 2011	Group: Database references
Revision 1.3	Sep 27, 2017	Group: Data collection / Category: pdbx_diffrn_reflns_shell / reflns_shell Item: _pdbx_diffrn_reflns_shell.percent_possible_obs / _reflns_shell.percent_possible_all
Revision 1.4	Nov 27, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qd5.cif.gz	137.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3qd5.ent.gz	105 KB	Display	PDB format
PDBx/mmJSON format	3qd5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3qd5_validation.pdf.gz	452.7 KB	Display	wwPDB validaton report
Full document	3qd5_full_validation.pdf.gz	454.6 KB	Display
Data in XML	3qd5_validation.xml.gz	19.1 KB	Display
Data in CIF	3qd5_validation.cif.gz	25.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qd/3qd5 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/3qd5	HTTPS FTP

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Related structure data

Related structure data	3sdwC 3sgwC C: citing same article (ref.)
Similar structure data	7c7g-2 3sdw-1 6pnl-d 2xy8-d 1b8u-d 4jpl-d 4wdw-1 6isq-1 6b7l-d 4e3o-2 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
Other databases	TargetDB: CoimA.00584.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: putative ribose-5-phosphate isomerase

B: putative ribose-5-phosphate isomerase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

2

A: putative ribose-5-phosphate isomerase

B: putative ribose-5-phosphate isomerase

hetero molecules

A: putative ribose-5-phosphate isomerase

B: putative ribose-5-phosphate isomerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	103.150, 49.890, 61.970
Angle α, β, γ (deg.)	90.00, 108.62, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-176- IOD
2	1	B-175- IOD

#1: Protein	putative ribose-5-phosphate isomerase Mass: 17734.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coccidioides immitis (fungus) / Strain: RS / Gene: CIMG_07932, 4559626 / Production host: Escherichia coli (E. coli) References: UniProt: P0CL19*PLUS, ribose-5-phosphate isomerase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	... ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: I
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H₂O
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: 2.13 Å³/Da / Density % sol: 42.26 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 Details: CoimA.00584.a.A1 PS00647 82 mg/mL against JCSG+ screen condition B9, 20% PEG 6000, 0.1 M Na Citrate pH 5.0, and soaked into 20% PEG 6000, 0.1 M Na Citrate pH 5.0, 0.7 M NaI, 22% ethylene ...Details: CoimA.00584.a.A1 PS00647 82 mg/mL against JCSG+ screen condition B9, 20% PEG 6000, 0.1 M Na Citrate pH 5.0, and soaked into 20% PEG 6000, 0.1 M Na Citrate pH 5.0, 0.7 M NaI, 22% ethylene glycol for one minute, crystal tracking ID 216516b9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal

Density Matthews: 2.13 Å³/Da / Density % sol: 42.26 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: CoimA.00584.a.A1 PS00647 82 mg/mL against JCSG+ screen condition B9, 20% PEG 6000, 0.1 M Na Citrate pH 5.0, and soaked into 20% PEG 6000, 0.1 M Na Citrate pH 5.0, 0.7 M NaI, 22% ethylene ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 11, 2011

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Number: 138436 / R_merge(I) obs: 0.042 / D res high: 1.9 Å / Num. obs: 45516 / % possible obs: 98.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs
1.9	1.95	2868	84.2	1	0.134
1.95	2	3353	99.2	1	0.11
2	2.06	3197	99.3	1	0.093
2.06	2.12	3136	99	1	0.088
2.12	2.19	3031	99.9	1	0.079
2.19	2.27	2964	99.5	1	0.069
2.27	2.36	2779	99.6	1	0.067
2.36	2.45	2781	99.6	1	0.067
2.45	2.56	2598	99.8	1	0.061
2.56	2.69	2499	99.6	1	0.057
2.69	2.83	2390	99.9	1	0.05
2.83	3	2242	99.6	1	0.045
3	3.21	2116	99.7	1	0.042
3.21	3.47	1975	100	1	0.038
3.47	3.8	1843	99.4	1	0.035
3.8	4.25	1602	100	1	0.032
4.25	4.91	1452	99.2	1	0.031
4.91	6.01	1234	100	1	0.033
6.01	8.5	938	99.3	1	0.03
8.5	50	518	98.9	1	0.032

Reflection

Resolution: 1.9→50 Å / Num. all: 23781 / Num. obs: 23513 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / R_merge(I) obs: 0.055 / Net I/σ(I): 20.49

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.9-1.95	2.9	0.152	6	1	87.5
1.95-2		0.137	7.4	1	99.7
2-2.06		0.114	9.7	1	99.7
2.06-2.12		0.106	11.5	1	99.7
2.12-2.19		0.096	13.9	1	100
2.19-2.27		0.086	15.8	1	99.7
2.27-2.36		0.084	17.5	1	99.9
2.36-2.45		0.082	18.5	1	99.8
2.45-2.56		0.077	21.4	1	99.9
2.56-2.69		0.073	22.5	1	99.6
2.69-2.83		0.064	23.7	1	99.8
2.83-3		0.06	25.9	1	99.7
3-3.21		0.056	28	1	99.7
3.21-3.47		0.049	31.7	1	100
3.47-3.8		0.044	36.5	1	99.5
3.8-4.25		0.041	38.6	1	100
4.25-4.91		0.042	39.2	1	99.3
4.91-6.01		0.046	35.6	1	100
6.01-8.5		0.044	36.2	1	99.4
8.5-50		0.044	38.3	1	98

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Phasing

Phasing

Method
SAD
molecular replacement

Phasing MAD

D res high: 1.9 Å / D res low: 44.44 Å / FOM : 0.527 / FOM acentric: 0.536 / FOM centric: 0.381 / Reflection: 23480 / Reflection acentric: 21981 / Reflection centric: 1268

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
9.03-12.51	0.658	0.693	0.502	147	120	27
7.42-9.03	0.632	0.653	0.494	183	159	24
6.45-7.42	0.686	0.692	0.649	216	186	30
5.78-6.45	0.64	0.651	0.54	246	220	26
5.28-5.78	0.637	0.651	0.524	268	238	30
4.9-5.28	0.629	0.645	0.495	290	262	27
4.59-4.9	0.647	0.664	0.505	306	275	30
4.33-4.59	0.661	0.683	0.395	331	305	26
4.11-4.33	0.611	0.629	0.426	340	310	29
3.92-4.11	0.59	0.605	0.394	367	341	26
3.75-3.92	0.58	0.597	0.403	375	344	30
3.6-3.75	0.574	0.594	0.327	392	362	29
3.47-3.6	0.621	0.639	0.311	413	390	23
3.36-3.47	0.569	0.582	0.416	415	383	32
3.25-3.36	0.589	0.602	0.384	432	406	26
3.15-3.25	0.577	0.59	0.364	465	437	28
3.07-3.15	0.564	0.58	0.305	456	429	26
2.98-3.07	0.575	0.591	0.338	474	444	30
2.91-2.98	0.597	0.605	0.482	483	456	25
2.84-2.91	0.59	0.61	0.251	489	462	25
2.77-2.84	0.58	0.596	0.35	526	493	33
2.71-2.77	0.572	0.581	0.338	521	500	21
2.66-2.71	0.573	0.591	0.331	538	503	33
2.6-2.66	0.583	0.59	0.478	536	510	25
2.55-2.6	0.572	0.585	0.347	565	534	31
2.51-2.55	0.602	0.61	0.435	568	543	25
2.46-2.51	0.566	0.573	0.398	555	528	24
2.42-2.46	0.542	0.552	0.354	606	574	31
2.38-2.42	0.519	0.523	0.425	556	530	24
2.34-2.38	0.545	0.556	0.342	644	610	31
2.3-2.34	0.528	0.537	0.342	602	575	23
2.27-2.3	0.522	0.53	0.394	620	589	27
2.23-2.27	0.505	0.514	0.302	642	617	23
2.2-2.23	0.506	0.517	0.272	645	612	29
2.17-2.2	0.49	0.495	0.345	646	624	22
2.14-2.17	0.488	0.492	0.38	653	617	30
2.11-2.14	0.458	0.469	0.241	689	647	31
2.09-2.11	0.444	0.451	0.288	660	628	23
2.06-2.09	0.443	0.452	0.266	690	650	30
2.03-2.06	0.445	0.449	0.337	696	664	26
2.01-2.03	0.422	0.425	0.3	716	683	23
1.99-2.01	0.412	0.413	0.371	675	641	28
1.96-1.99	0.427	0.43	0.36	748	716	24
1.94-1.96	0.395	0.404	0.239	729	671	29
1.92-1.94	0.415	0.425	0.336	660	575	21
1.9-1.92	0.401	0.404	0.338	612	552	26

Phasing MR

R_factor: 54.44 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3 Å	33.19 Å
Translation	3 Å	33.19 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.1.4	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
StructureStudio		data collection
XDS		data reduction

Refinement

Method to determine structure:

SAD,

MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.933 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.813 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1527 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20508	1205	5.1 %	RANDOM
R_work	0.16423	-	-	-
obs	0.16637	22275	98.87 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 18.317 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.11 Å²	0 Å²	-0.08 Å²
2-	-	-0.39 Å²	0 Å²
3-	-	-	-0.77 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2369	0	37	213	2619

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2456
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.364	1.969	3345
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.517	5.235	340
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.448	24.286	91
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.031	15	404
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.156	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	407
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1810
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	0.729	1.5	1612
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.313	2	2594
X-RAY DIFFRACTION	r_scbond_it	2.329	3	844
X-RAY DIFFRACTION	r_scangle_it	3.778	4.5	744
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.242	81	-
R_work	0.185	1434	-
obs	-	-	87.42 %

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	0.2894	-0.1113	-0.0407	0.7335	0.2273	0.3365	-0.0113	-0.0222	0.0008	-0.06	0.0279	0.0745	-0.0389	-0.0225	-0.0166	0.0162	0.0065	-0.001	0.0161	0.0149	0.0207	30.2803	10.1056	16.8113
2	0.4193	0.0459	0.0006	0.6069	-0.0629	0.2319	-0.003	-0.0009	-0.0282	-0.0736	0.0309	-0.0123	0.0178	0.0031	-0.0279	0.0241	-0.0058	0.0004	0.0121	-0.0091	0.0119	42.2236	-7.3692	12.0159

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 9999
2	X-RAY DIFFRACTION	2	B	-10 - 9999

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