PDB-3tj4: Crystal structure of an enolase from agrobacterium tumefaciens (e...

ID or keywords:

Entry

Database: PDB / ID: 3tj4

Title

Crystal structure of an enolase from agrobacterium tumefaciens (efi target efi-502087) no mg

Components

Mandelate racemase

Keywords

LYASE / Enolase / dehydratase / enzyme function initiative / EFI / Structural Genomics

Function / homology

Function and homology information

hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function

Biological species

Agrobacterium tumefaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 1.5 Å

Authors

Vetting, M.W. / Bouvier, J.T. / Wasserman, S.R. / Morisco, L.L. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)

Citation

Journal: to be published
Title: Crystal structure of an enolase from agrobacterium tumefaciens (efi target efi-502087) no mg
Authors: Vetting, M.W. / Bouvier, J.T. / Wasserman, S.R. / Morisco, L.L. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)

History

Deposition	Aug 23, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 14, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 12, 2011	Group: Structure summary
Revision 1.2	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3	Sep 13, 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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3tj4.cif.gz	297.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3tj4.ent.gz	238.7 KB	Display	PDB format
PDBx/mmJSON format	3tj4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tj4_validation.pdf.gz	451.4 KB	Display	wwPDB validaton report
Full document	3tj4_full_validation.pdf.gz	454.5 KB	Display
Data in XML	3tj4_validation.xml.gz	35.6 KB	Display
Data in CIF	3tj4_validation.cif.gz	56.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tj/3tj4 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/3tj4	HTTPS FTP

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Related structure data

Related structure data	3cb3S S: Starting model for refinement
Similar structure data	4h19-3 4gme-1 2gl5-1 4h19-1 3vcn-2 3dfy-2 3sjn-1 2poz-d 4e5t-d 4h19-2 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	TargetTrack: EFI-502087

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (2)

Deposited unit

A: Mandelate racemase

B: Mandelate racemase

hetero molecules

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

1

A: Mandelate racemase

B: Mandelate racemase

hetero molecules

A: Mandelate racemase

B: Mandelate racemase

hetero molecules

A: Mandelate racemase

B: Mandelate racemase

hetero molecules

A: Mandelate racemase

B: Mandelate racemase

hetero molecules

defined by author&software
335 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	118.739, 118.739, 113.423
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	90
Space group name H-M	P42₁2

Details

biological unit is an octamer

#1: Protein	Mandelate racemase Mass: 41123.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_L_1470, Atu4120 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7CU39
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 957 / 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: 2.43 Å³/Da / Density % sol: 49.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (0.4 M AmPO4 monobasic); Cryoprotection (Reservoir + 20% glycerol), sitting drop vapor diffuction, ...Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (0.4 M AmPO4 monobasic); Cryoprotection (Reservoir + 20% glycerol), sitting drop vapor diffuction, temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal

Density Matthews: 2.43 Å³/Da / Density % sol: 49.39 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (0.4 M AmPO4 monobasic); Cryoprotection (Reservoir + 20% glycerol), sitting drop vapor diffuction, ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 1, 2011 / Details: MIRRORS
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.5→40 Å / Num. all: 127613 / Num. obs: 127613 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / B_iso Wilson estimate: 7.61 Å² / R_merge(I) obs: 0.069 / R_sym value: 0.069 / Net I/σ(I): 22.2
Reflection shell	Resolution: 1.5→1.58 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.32 / Mean I/σ(I) obs: 4.6 / Num. unique all: 17126 / R_sym value: 0.32 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
PHENIX	1.7_650	refinement
PDB_EXTRACT	3.1	data extraction
MAR345dtb		data collection
MOSFLM		data reduction
SCALA		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MIR
Starting model: PDB entry 3CB3

3cb3

Resolution: 1.5→40 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.9245 / SU ML: 0.16 / σ(F): 0 / Phase error: 13.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1654	6225	5.03 %	random
R_work	0.148	-	-	-
all	0.1489	123677	-	-
obs	0.1489	123677	95.64 %	-

Solvent computation

Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 28.651 Å² / k_sol: 0.364 e/Å³

Displacement parameters

B_iso max: 63.35 Å² / B_iso mean: 9.8967 Å² / B_iso min: 1.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.3323 Å²	0 Å²	-0 Å²
2-	-	0.3323 Å²	-0 Å²
3-	-	-	-0.6646 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5640	0	79	957	6676

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6014
X-RAY DIFFRACTION	f_angle_d	1.074	8233
X-RAY DIFFRACTION	f_chiral_restr	0.068	905
X-RAY DIFFRACTION	f_plane_restr	0.006	1052
X-RAY DIFFRACTION	f_dihedral_angle_d	11.572	2123

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5-1.517	0.1904	171	0.1782	3243	3414	80
1.517-1.5349	0.2146	188	0.1854	3347	3535	83
1.5349-1.5536	0.1916	176	0.1742	3530	3706	87
1.5536-1.5733	0.1863	208	0.1661	3601	3809	90
1.5733-1.594	0.2026	205	0.1638	3744	3949	92
1.594-1.6158	0.1801	192	0.1612	3802	3994	94
1.6158-1.6389	0.2063	185	0.1587	3907	4092	96
1.6389-1.6634	0.1868	226	0.149	3902	4128	97
1.6634-1.6894	0.1704	217	0.1449	3937	4154	97
1.6894-1.7171	0.162	215	0.1358	3953	4168	98
1.7171-1.7467	0.1595	201	0.1345	4023	4224	98
1.7467-1.7784	0.1466	226	0.128	3898	4124	98
1.7784-1.8127	0.1489	219	0.1251	3988	4207	98
1.8127-1.8497	0.1652	209	0.1267	4014	4223	99
1.8497-1.8899	0.1472	202	0.1369	3943	4145	97
1.8899-1.9338	0.2671	186	0.235	3550	3736	87
1.9338-1.9822	0.1602	205	0.1365	3944	4149	97
1.9822-2.0358	0.161	206	0.1371	4047	4253	99
2.0358-2.0957	0.1465	206	0.1353	4064	4270	100
2.0957-2.1634	0.1529	176	0.1445	4100	4276	99
2.1634-2.2407	0.1617	190	0.1579	3849	4039	94
2.2407-2.3304	0.2034	202	0.205	3877	4079	94
2.3304-2.4365	0.1728	232	0.1383	4063	4295	100
2.4365-2.5649	0.1575	220	0.1384	4101	4321	100
2.5649-2.7257	0.1653	209	0.1431	4125	4334	100
2.7257-2.9361	0.1534	205	0.1436	4141	4346	100
2.9361-3.2316	0.1598	243	0.1451	4133	4376	100
3.2316-3.6992	0.1485	237	0.1383	4124	4361	99
3.6992-4.6606	0.1379	228	0.1186	4203	4431	99
4.6606-84.0929	0.1531	240	0.1576	4299	4539	97

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	0.0128	-0.0044	0.0242	0.0669	0.016	0.0739	0.0341	-0.0166	0.0006	0.0083	-0.0067	-0.0416	0.0115	-0.0198	-0.0234	0.0397	0.0116	-0.0105	0.0602	-0.0066	0.0456	28.6602	21.4166	32.1161
2	0.0301	-0.0167	0.0412	0.0242	-0.0125	0.0635	0.0233	-0.0192	-0.0024	-0.0093	0.0093	-0.024	0.0169	-0.0142	-0.0183	0.0318	0.0064	-0.0089	0.0426	-0.0143	0.0436	26.4694	22.6131	25.9605
3	0.0015	0	-0.0006	0.0004	0.0003	0.0007	0	0.0143	0.0001	-0.0115	0.0025	0.0006	0.0018	-0.0072	-0.0019	0.0453	0.0132	-0.0035	0.0529	-0.008	0.0369	21.0402	31.12	16.3188
4	0.0001	-0.0002	-0.0014	0.0006	0.003	0.0159	0.0077	-0.0042	0.0044	-0.0012	0.0108	-0.0012	0.0042	0.0125	-0.008	0.0148	0.0077	-0.0065	0.0306	-0.0127	0.0295	32.5885	36.4039	30.9517
5	0.0003	0	-0.001	0.0011	-0.0009	0.004	-0.0032	-0.0133	-0.0061	0.007	0.0026	-0.0022	0.0018	0.0025	-0	0.0442	0.0072	-0.0184	0.0423	0.0124	0.0351	16.1344	35.4049	57.1668
6	0.0296	-0.024	0.0126	0.0451	-0.018	0.0336	-0.0004	-0.0099	-0.0094	0.0105	0.0078	0.009	-0.0043	-0.0055	-0.0022	0.0183	0.0006	-0.009	0.0272	0.003	0.017	9.2473	43.2306	51.8379
7	0.0058	0.0038	0.0005	0.0025	0.0005	0.0009	0.0001	0.0027	0.0025	-0.0021	-0.0014	-0.0003	0.0034	-0.0067	0.0012	0.0323	0.0045	-0.0012	0.0434	-0.0006	0.0375	3.4863	44.4455	35.4533
8	0.0154	0.0011	-0.005	0.0049	0.0036	0.0049	0.0103	0.0022	-0.0076	0.0077	0.0101	-0.0045	0.01	0.0042	-0.0033	0.0158	0.0053	-0.0072	0.014	0.0016	0.0152	20.0395	42.2438	34.9172
9	0.0005	0.0003	0	0.0035	-0.0009	0.0007	-0.0013	-0.0054	-0.0007	0.0025	0.0018	-0.0025	0.003	0.0023	-0.0005	0.041	0.0179	-0.0179	0.0406	-0.0015	0.036	33.7662	34.4438	46.6574
10	0.0028	0.0021	0.0017	0.0107	-0.003	0.003	0.0112	-0.0064	-0.0204	-0.0037	0.008	0.0075	0.0226	-0.0112	0.0028	0.0612	0.0109	-0.0291	0.0406	0.0057	0.051	31.9946	21.1537	38.5898
11	0.1329	0.0363	-0.0457	0.1016	0.0508	0.0867	0.0162	-0.0214	-0.0349	-0.0321	0.0171	-0.0348	-0.0247	0.009	-0.0296	0.0468	0.0089	0.008	0.0544	-0.0127	0.0523	47.4489	61.8797	16.9353
12	0.0739	0.0411	-0.0127	0.0268	0.0089	0.0909	0.0318	-0.0069	-0.0312	-0.0025	-0.0056	-0.0229	-0.0213	0.0376	-0.026	0.0369	0.0076	0.0001	0.048	-0.0156	0.0514	45.235	62.8373	23.2581
13	0.0065	0.0003	0.0001	0.0018	0.0029	0.0102	0.0011	-0.0124	-0.0021	0.003	0.0055	-0.0029	-0.0007	-0.0015	-0.0042	0.0104	0.0035	-0.0015	0.0353	-0.0095	0.0193	35.023	61.5829	32.6938
14	0.0207	-0.0189	-0.0114	0.0391	-0.0097	0.0248	0.0126	-0.0124	0.0152	-0.0075	-0.008	0.0028	0.0094	0.0132	-0.0022	0.0272	0.0098	-0.0003	0.0342	-0.014	0.0362	38.6062	49.5717	18.2924
15	0.0084	0.002	-0.0029	0.0025	-0.0028	0.0032	-0.0009	0.0114	0.0038	-0.0101	0.0009	-0.0072	0.003	0.0043	-0.0011	0.0409	0.0029	0.0239	0.0547	0.0061	0.0384	28.9594	62.5251	-7.5305
16	0.0304	-0.0109	0.0085	0.055	-0.01	0.0033	0.0096	0.0106	0.0091	-0.0188	-0.0009	0.0004	0.0098	-0.0017	-0.0006	0.0264	0.009	0.0072	0.0228	-0.0052	0.02	18.1116	63.0279	-2.5413
17	0.005	0.0006	0.0033	0.0002	0.0001	0.0026	0.0058	-0.0072	0.001	-0.0029	0.0061	0.0032	-0.0045	-0.0029	-0.0102	0.0217	0.0052	0.0019	0.0266	-0.0042	0.0321	13.6037	66.361	13.6303
18	0.002	0.0014	0.0028	0.0022	0.0016	0.0041	0.0045	-0.0022	0.0047	-0.0013	0.0093	-0.011	-0.0043	0.0072	0.0104	0.0127	0.0057	0.006	0.0199	-0.0046	0.0182	26.0329	55.1476	14.2332
19	0.0072	0.0032	0.0055	0.0056	0.0018	0.0045	0.0115	0.0055	0.0131	-0.0049	0.0014	-0.0095	-0.0121	0.0122	0.002	0.0243	0.0012	0.0156	0.0516	-0.0133	0.0385	45.661	54.5645	6.8659

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:39)	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 40:80)	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 81:100)	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 101:139)	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 140:164)	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 165:229)	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 230:246)	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 247:332)	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 333:350)	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 351:372)	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 1:39)	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 40:80)	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 81:101)	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 102:139)	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 140:164)	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 165:229)	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 230:246)	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 247:332)	B
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 333:372)	B

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi