PDB-3uw1: Crystal structure of ribose-5-phosphate isomerase a from burkhold...

Basic information

• Entry: Database: PDB / ID: 3uw1
• Title: Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate
• Components: Ribose-5-phosphate isomerase A
• Keywords: ISOMERASE / SSGCID / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Ribose isomerase / Ribose-5-phosphate

Function / homology

Function:

D-ribose metabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / cytosol

Domain/homology:

Ribose-5-phosphate isomerase, type A, subgroup / Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) / Rossmann fold - #1360 / ACT domain / NagB/RpiA transferase-like / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta

Component:

RIBOSE-5-PHOSPHATE / Ribose-5-phosphate isomerase A

• Biological species: Burkholderia thailandensis (bacteria)
• Method: X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
• Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Citation: Journal: Plos One / Year: 2013; Title: Combining functional and structural genomics to sample the essential Burkholderia structome.; Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.

History

Deposition	Nov 30, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 21, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2013	Group: Database references
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Ribose-5-phosphate isomerase A

hetero molecules

Summary:

• 25.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	25,365	2
Polymers	25,135	1
Non-polymers	230	1
Water	4,972	276

1

A: Ribose-5-phosphate isomerase A

hetero molecules

A: Ribose-5-phosphate isomerase A

hetero molecules

Summary:

• defined by author&software
• 50.7 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,730	4
Polymers	50,269	2
Non-polymers	460	2
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_757	-x+2,y,-z+2	1

Calculated values:

Buried area	3310 Å2
ΔGint	-16 kcal/mol
Surface area	18760 Å2
Method	PISA

2

A: Ribose-5-phosphate isomerase A

hetero molecules

A: Ribose-5-phosphate isomerase A

hetero molecules

Summary:

• defined by software
• 50.7 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,730	4
Polymers	50,269	2
Non-polymers	460	2
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_758	-x+2,y,-z+3	1

Calculated values:

Buried area	2790 Å2
ΔGint	-15 kcal/mol
Surface area	19280 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	80.420, 73.558, 52.032
Angle α, β, γ (deg.)	90.00, 127.97, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-390- HOH

Components

#1: Protein

A Ribose-5-phosphate isomerase A / Phosphoriboisomerase A

Details:

Mass: 25134.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I2516, rpiA / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SVL4, ribose-5-phosphate isomerase

#2: Sugar

A-400 ChemComp-R5P / RIBOSE-5-PHOSPHATE

Details:

Type: saccharide / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₅H₁₁O₈P

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.41 ų/Da / Density % sol: 49.04 %
• Crystal grow: Temperature: 290 K / pH: 6.5 ; Details: Internal tracking number 225985D11. WIZARD 3/4 screen condition D11: 30%(w/v) PEG 5000 MME, 0.1M MES, 0.2M Ammonium sulfate, ButhA.00944.a.A1 PW33411 at 33.6 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 6.5

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178
• Detector: Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 11, 2011
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.54178 Å / Relative weight: 1
• Reflection: Redundancy: 7.1 % / Av σ(I) over netI: 23.9 / Number: 183213 / R_merge(I) obs: 0.076 / Χ²: 0.92 / D res high: 1.71 Å / D res low: 50 Å / Num. obs: 25863 / % possible obs: 99.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	Rmerge(I) obs	Chi squared	Redundancy
4.64	50	99.6	1	0.065	0.668	11.1
3.68	4.64	100	1	0.063	0.612	11.2
3.22	3.68	100	1	0.068	0.691	11.2
2.92	3.22	100	1	0.076	0.719	11.2
2.71	2.92	100	1	0.084	0.823	10.4
2.55	2.71	100	1	0.092	0.956	8.8
2.43	2.55	100	1	0.094	1.019	8
2.32	2.43	100	1	0.099	1.19	7.6
2.23	2.32	100	1	0.106	1.327	7.2
2.15	2.23	100	1	0.113	1.479	6.9
2.09	2.15	100	1	0.113	1.542	6.3
2.03	2.09	100	1	0.101	1.222	5.6
1.97	2.03	100	1	0.086	0.862	5.1
1.93	1.97	100	1	0.096	0.836	4.9
1.88	1.93	100	1	0.103	0.81	4.7
1.84	1.88	100	1	0.106	0.781	4.6
1.81	1.84	100	1	0.12	0.814	4.4
1.77	1.81	100	1	0.132	0.848	4.3
1.74	1.77	99.6	1	0.151	0.902	4.1
1.71	1.74	89.5	1	0.155	0.86	3.1

• Reflection: Resolution: 1.71→50 Å / Num. obs: 25863 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / R_merge(I) obs: 0.076 / Net I/σ(I): 19.9
• Reflection shell: Resolution: 1.71→1.74 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.155 / % possible all: 89.5

Phasing

• Phasing: Method: molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.5 Å	27.38 Å
Translation	2.5 Å	27.38 Å

Processing

Software

Name	Version	Classification	NB
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.3.0	phasing
PHENIX	1.7.2_869	refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→27.38 Å / Occupancy max: 99 / Occupancy min: 0 / SU ML: 0.37 / σ(F): 0 / Phase error: 15.12 / Stereochemistry target values: ML

	Rfactor	Num. reflection	% reflection
Rfree	0.173	1263	4.97 %
Rwork	0.147	-	-
obs	0.149	25399	97.7 %

• Solvent computation: Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / k_sol: 0.34 e/ų
• Displacement parameters: B_iso mean: 14.35 Ų

Refinement step

Cycle: LAST / Resolution: 1.71→27.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1705	0	14	276	1995

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	1796
X-RAY DIFFRACTION	f_angle_d	1.296	2439
X-RAY DIFFRACTION	f_dihedral_angle_d	11.286	666
X-RAY DIFFRACTION	f_chiral_restr	0.079	286
X-RAY DIFFRACTION	f_plane_restr	0.006	322

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.7067-1.775	0.1933	135	0.1638	2414	X-RAY DIFFRACTION	89
1.775-1.8558	0.1659	134	0.1428	2651	X-RAY DIFFRACTION	96
1.8558-1.9536	0.1862	136	0.1413	2641	X-RAY DIFFRACTION	98
1.9536-2.076	0.1628	145	0.144	2704	X-RAY DIFFRACTION	98
2.076-2.2362	0.2079	140	0.1316	2711	X-RAY DIFFRACTION	99
2.2362-2.4611	0.159	147	0.1385	2735	X-RAY DIFFRACTION	99
2.4611-2.8169	0.1592	140	0.1437	2727	X-RAY DIFFRACTION	99
2.8169-3.5478	0.1686	140	0.154	2745	X-RAY DIFFRACTION	100
3.5478-27.3868	0.1721	146	0.1573	2808	X-RAY DIFFRACTION	100

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	3.2766	-1.0025	-1.2116	0.9162	0.4556	0.4912	-0.0785	-0.4328	0.0896	0.2453	0.035	-0.0272	-0.0194	0.1314	0.0451	0.0915	0.0021	-0.0211	0.1018	0.0066	0.0593	51.1421	60.184	74.1633
2	2.5368	-0.5027	-0.2919	0.7957	-0.3282	0.8878	-0.0282	-0.1788	0.1697	0.2333	0.0455	-0.0792	-0.1447	0.1031	-0.0104	0.0502	-0.0123	-0.0188	0.0368	-0.0105	0.0722	59.253	65.6357	67.3977
3	0.6621	-0.4635	0.0766	2.6106	0.7054	2.4239	-0.0067	0.0119	0.0788	0.077	0.0555	-0.0666	-0.1351	0.1502	-0.0401	0.0593	-0.0242	-0.02	0.0481	0.003	0.0739	60.9813	69.2017	59.0479
4	2.2632	0.5876	-0.2966	0.8177	-0.2904	1.899	-0.0184	-0.0006	0.0187	-0.0034	0.0452	0.0074	-0.0148	0.0541	-0.021	0.0299	0.0053	-0.0083	0.026	-0.0082	0.0294	49.3885	57.6928	58.5726
5	0.9818	0.0353	0.0727	1.1124	-0.3715	1.9686	0.0145	0.0347	0.2068	-0.0324	-0.0642	-0.0364	-0.1717	-0.0354	0.0243	0.0427	0.0096	0.0006	0.0453	-0.0004	0.0642	36.7757	62.3493	47.8008
6	0.7654	-0.239	0.1865	0.4968	0.2759	1.9566	0.0247	0.0276	-0.0191	-0.0136	0.0101	0.0151	0.1045	0.0312	-0.0375	0.0347	-0.0134	0.0053	0.0251	0.0029	0.0344	44.4366	52.4244	55.6274

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 4:25)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 26:53)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 54:85)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 86:129)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 130:179)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 180:234)