PDB-5vr0: Crystal structure of glucose isomerase from Streptomyces rubiginosus

ID or keywords:

Entry

Database: PDB / ID: 5vr0

Title

Crystal structure of glucose isomerase from Streptomyces rubiginosus

Components

Xylose isomerase

Keywords

ISOMERASE / Oxidoreductase / ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) / radiation damage

Function / homology

Function and homology information

xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Streptomyces rubiginosus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.7 Å

Authors

Borek, D. / Otwinowski, Z.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01GM118619	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01GM117080	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01GM053163	United States

Citation

Journal: J Synchrotron Radiat / Year: 2018
Title: Real-space analysis of radiation-induced specific changes with independent component analysis.
Authors: Borek, D. / Bromberg, R. / Hattne, J. / Otwinowski, Z.

History

Deposition	May 9, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 2, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 20, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5vr0.cif.gz	181.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5vr0.ent.gz	144.9 KB	Display	PDB format
PDBx/mmJSON format	5vr0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5vr0_validation.pdf.gz	443.4 KB	Display	wwPDB validaton report
Full document	5vr0_full_validation.pdf.gz	446.5 KB	Display
Data in XML	5vr0_validation.xml.gz	22.2 KB	Display
Data in CIF	5vr0_validation.cif.gz	34.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vr/5vr0 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/5vr0	HTTPS FTP

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Related structure data

Related structure data	1xibS S: Starting model for refinement
Similar structure data	4qe5-1 6rnd-1 3kcj-1 1qt1-1 6oqz-1 4hhl-1 8xia-1 1xij-1 1dxi-1 4duo-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (7)

Deposited unit

A: Xylose isomerase

hetero molecules

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

1

A: Xylose isomerase

hetero molecules

A: Xylose isomerase

hetero molecules

A: Xylose isomerase

hetero molecules

A: Xylose isomerase

hetero molecules

defined by author&software
Evidence: SAXS
176 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.854, 98.061, 102.279
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-838- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Xylose isomerase Mass: 43283.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Escherichia coli (E. coli) / References: UniProt: P24300, xylose isomerase

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Non-polymers , 5 types, 507 molecules

#2: Chemical	ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M CaCl2, 16-22% MPD (v/v) and 0.1 M Tris-HCl pH 7.0

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Data collection

Diffraction

Mean temperature: 100 K
Ambient temp details: The deposited F_AVE were obtained by averaging data sets acquired at 15, 40, 80, 100, 130 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9792, 1.5406

Detector

Type: SBC-3 / Detector: CCD / Date: Jan 1, 2001

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9792	1
2	1.5406	1

Reflection

Resolution: 1.7→50.01 Å / Num. obs: 49609 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 43.1 % / CC_1/2: 1 / R_pim(I) all: 0.013 / Net I/σ(I): 125

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0222	refinement
HKL-2000		data reduction
HKL-3000		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 1XIB

1xib

Resolution: 1.7→38.9 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.965 / SU B: 1.957 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.14161	2547	5 %	RANDOM
R_work	0.11877	-	-	-
obs	0.11988	48877	99.08 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 10.813 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.16 Å²	0 Å²	0 Å²
2-	-	0.43 Å²	-0 Å²
3-	-	-	-0.28 Å²

Refinement step

Cycle: 1 / Resolution: 1.7→38.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3046	0	25	489	3560

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.015	3356
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2884
X-RAY DIFFRACTION	r_angle_refined_deg	1.333	1.779	4574
X-RAY DIFFRACTION	r_angle_other_deg	0.495	1.762	6792
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.441	5	429
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.983	18.593	199
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.02	15	475
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.483	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	405
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	4043
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	665
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	0.587	0.476	1646
X-RAY DIFFRACTION	r_mcbond_other	0.587	0.477	1647
X-RAY DIFFRACTION	r_mcangle_it	0.971	0.711	2084
X-RAY DIFFRACTION	r_mcangle_other	0.964	0.711	2084
X-RAY DIFFRACTION	r_scbond_it	1.122	0.598	1710
X-RAY DIFFRACTION	r_scbond_other	1.122	0.599	1711
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.812	0.857	2486
X-RAY DIFFRACTION	r_long_range_B_refined	4.657	7.541	4031
X-RAY DIFFRACTION	r_long_range_B_other	4.054	6.344	3868
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.156	162	-
R_work	0.121	3518	-
obs	-	-	97.9 %

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	5.3185	2.77	2.6487	1.8497	0.6338	2.6907	0.1772	-0.2511	0.1166	0.0725	-0.1679	0.0978	0.1429	-0.0742	-0.0093	0.0672	-0.0311	0.0248	0.0526	-0.0088	0.0226	33.2242	34.7452	29.1279
2	1.5113	0.0021	-0.1746	0.0286	-0.0465	0.1058	-0.0424	0.1125	-0.0922	0.0076	0.0124	0.002	0.0044	-0.0229	0.03	0.0485	-0.0197	0.0197	0.0614	-0.0034	0.057	43.3442	25.7333	9.4782
3	1.2316	0.255	-1.6058	1.3649	0.636	2.8091	0.0104	-0.07	-0.0899	0.0753	-0.0706	-0.0856	0.0338	0.0514	0.0602	0.0507	-0.003	0.0132	0.0374	0.0265	0.0661	37.6787	19.0953	20.0273
4	0.0747	0.1282	-0.107	0.6403	0.5945	1.6066	-0.0073	-0.0115	-0.0138	0.0296	-0.038	-0.0103	0.117	-0.0311	0.0453	0.0593	-0.0153	0.0165	0.0493	0.0014	0.0517	31.183	22.1849	12.2132
5	0.7277	-0.1387	0.2757	2.247	0.9897	7.68	-0.1084	-0.0243	-0.1296	-0.0136	0.0432	-0.0156	0.4052	-0.1008	0.0653	0.0838	-0.0286	0.0385	0.0209	-0.011	0.0529	26.5476	10.0355	10.4202
6	0.0605	0.0686	-0.0652	0.1963	-0.2748	0.7729	-0.0217	-0.0001	-0.0274	-0.0114	-0.0344	0.0137	0.0522	-0.0046	0.0561	0.0504	-0.0183	0.019	0.0509	-0.0142	0.0685	27.1743	24.1024	2.2198
7	1.6016	0.5827	-1.5143	1.8732	-0.2642	2.6778	0.0216	-0.1369	-0.1115	-0.0914	-0.0438	-0.0818	0.0291	-0.0509	0.0222	0.0502	-0.0317	0.0144	0.0496	0.0065	0.0534	20.7949	21.3865	6.3537
8	3.0673	-3.0349	1.0011	5.318	-4.109	4.5296	-0.0117	0.0075	-0.0828	0.1027	0.0078	0.0653	-0.1099	-0.0278	0.0039	0.0715	-0.0699	0.0276	0.111	-0.0065	0.027	19.4745	24.0862	14.1478
9	0.1573	-0.0725	-0.0764	0.0472	0.0094	0.2887	-0.0026	0.0124	-0.0212	-0.0149	-0.0206	0.0165	0.0221	-0.0233	0.0231	0.0486	-0.0138	0.0021	0.0577	-0.0188	0.0585	23.9977	34.4407	-5.3259
10	1.2095	0.8337	-0.2549	0.6057	0.1721	3.9443	0.107	-0.1527	0.0553	0.0758	-0.1241	0.0417	0.0001	-0.1839	0.0171	0.0179	-0.0236	0.0245	0.0753	-0.0009	0.0712	13.7257	29.0853	9.361
11	0.1773	-0.0689	-0.1465	0.3052	-0.0821	0.1959	0.0191	0.0122	-0.0017	-0.0048	-0.0285	0.0117	-0.006	-0.0044	0.0094	0.0482	-0.0069	0.0028	0.0559	-0.0138	0.0529	30.1918	40.3231	-0.4612
12	1.5818	1.4638	0.3175	1.7046	0.1643	2.6717	-0.0127	-0.0736	0.0733	-0.0512	-0.0287	0.1097	0.1089	-0.2929	0.0414	0.0107	-0.0045	-0.0039	0.0794	-0.0277	0.0668	14.6665	40.2796	0.8799
13	0.7015	-0.059	-0.1029	0.4533	0.1575	0.0655	0.0121	-0.0175	-0.0152	-0.0104	-0.0235	0.0119	-0.0053	-0.0106	0.0114	0.0476	-0.006	0.0062	0.0561	-0.0054	0.0465	30.9272	44.5799	9.7858
14	2.0071	-1.3546	1.9047	0.9557	-1.0699	3.1156	0.0527	0.1659	-0.0062	-0.0276	-0.0882	0.0025	-0.0131	0.3061	0.0356	0.0607	-0.0202	-0.0088	0.061	-0.0001	0.0386	45.7958	39.7192	8.099
15	0.3131	0.004	0.162	0.6554	0.1167	0.1365	-0.0277	-0.0392	-0.0109	0.0306	-0.0074	0.0075	-0.0075	-0.0175	0.0351	0.0466	-0.0065	0.0129	0.0533	-0.0026	0.0505	34.5616	43.8308	18.7328
16	0.1552	-0.1321	-0.0698	0.4261	0.1704	0.1296	-0.0035	-0.0402	-0.0439	0.0403	-0.0239	0.0285	0.0035	-0.0067	0.0273	0.0561	-0.0059	0.0078	0.0518	0.0045	0.0442	41.2747	37.5922	22.8693
17	0.6769	-1.7253	0.964	4.7953	-1.5985	3.5751	-0.0484	-0.0005	0.008	0.1496	0.011	0.0388	-0.0597	0.0565	0.0374	0.0537	0.0029	0.0159	0.0513	-0.0191	0.0402	32.7282	63.6532	29.2365
18	0.9783	-0.1405	0.6089	0.6573	-0.5728	0.7931	-0.057	-0.1045	0.0737	0.1113	0.0065	0.0465	-0.121	-0.0946	0.0505	0.051	0.0308	0.0019	0.0548	-0.0446	0.0631	21.6913	75.0796	12.195
19	0.339	-0.3053	0.4619	1.1021	-0.429	0.6353	-0.0169	-0.0161	0.0319	0.0655	-0.0265	0.0068	-0.0352	-0.0078	0.0434	0.0552	-0.0012	0.0018	0.0587	-0.0165	0.0458	39.5408	64.5961	22.2709
20	2.1003	-1.3968	-0.5771	5.6566	2.217	4.3154	0.0286	-0.1128	-0.0412	0.2356	0.0142	-0.0561	0.2654	0.0595	-0.0428	0.0427	-0.0059	-0.0085	0.0458	-0.0001	0.0116	44.8072	53.9334	29.2295

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 11
2	X-RAY DIFFRACTION	2	A	12 - 31
3	X-RAY DIFFRACTION	3	A	32 - 45
4	X-RAY DIFFRACTION	4	A	46 - 62
5	X-RAY DIFFRACTION	5	A	63 - 74
6	X-RAY DIFFRACTION	6	A	75 - 120
7	X-RAY DIFFRACTION	7	A	121 - 126
8	X-RAY DIFFRACTION	8	A	127 - 132
9	X-RAY DIFFRACTION	9	A	133 - 171
10	X-RAY DIFFRACTION	10	A	172 - 177
11	X-RAY DIFFRACTION	11	A	178 - 203
12	X-RAY DIFFRACTION	12	A	204 - 212
13	X-RAY DIFFRACTION	13	A	213 - 249
14	X-RAY DIFFRACTION	14	A	250 - 259
15	X-RAY DIFFRACTION	15	A	260 - 288
16	X-RAY DIFFRACTION	16	A	289 - 323
17	X-RAY DIFFRACTION	17	A	324 - 331
18	X-RAY DIFFRACTION	18	A	332 - 366
19	X-RAY DIFFRACTION	19	A	367 - 382
20	X-RAY DIFFRACTION	20	A	383 - 388

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Sample preparation

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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