PDB-3e02: Crystal structure of a duf849 family protein (bxe_c0271) from bur...

Basic information

• Entry: Database: PDB / ID: 300
• Title: Crystal structure of a duf849 family protein (bxe_c0271) from burkholderia xenovorans lb400 at 1.90 A resolution
• Components: uncharacterized protein DUF849
• Keywords: METAL BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2

Function / homology

Function:

3-keto-5-aminohexanoate cleavage activity / metal ion binding

Domain/homology:

3-keto-5-aminohexanoate cleavage enzyme / beta-keto acid cleavage enzyme / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta

Component:

3-keto-5-aminohexanoate cleavage protein

• Biological species: Burkholderia xenovorans LB400 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
• Authors: Joint Center for Structural Genomics (JCSG)
• Citation: Journal: To be published; Title: Crystal structure of protein of unknown function (DUF849) (YP_555544.1) from BURKHOLDERIA XENOVORANS LB400 at 1.90 A resolution; Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Jul 30, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 12, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Feb 1, 2023	Group: Database references / Derived calculations / Category: 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
Revision 1.5	Oct 30, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Assembly

Deposited unit

A: uncharacterized protein DUF849

hetero molecules

Summary:

• 35.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	35,448	12
Polymers	34,762	1
Non-polymers	686	11
Water	5,603	311

1

A: uncharacterized protein DUF849

hetero molecules

A: uncharacterized protein DUF849

hetero molecules

A: uncharacterized protein DUF849

hetero molecules

A: uncharacterized protein DUF849

hetero molecules

Summary:

• defined by author&software
• 142 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	141,792	48
Polymers	139,047	4
Non-polymers	2,744	44
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_765	-x+2,-y+1,z	1
crystal symmetry operation	9_765	-x+2,-x+y+1,-z+1/3	1
crystal symmetry operation	12_555	x,x-y,-z+1/3	1

Calculated values:

Buried area	9910 Å2
ΔGint	-168 kcal/mol
Surface area	40300 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	103.837, 103.837, 128.969
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	180
Space group name H-M	P6222

• Details: AUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

Components

#1: Protein

A uncharacterized protein DUF849

Details:

Mass: 34761.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans LB400 (bacteria)
Gene: YP_555544.1, Bxeno_C0266, Bxe_C0271 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13I95

#2: Chemical

A-311 ChemComp-ZN / ZINC ION

Details:

Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

#3: Chemical

A-312 A-313 A-314 A-315 A-316 A-317 A-318 A-319 A-320 A-321
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Details:

Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H₂O

• Has protein modification: Y
• Sequence details: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.89 ų/Da / Density % sol: 57.39 %
• Crystal grow: Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 ; Details: 1.0000M K/Na Tartrate, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97934,0.97892
• Detector: Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 16, 2008 / Details: Flat collimating mirror, toroid focusing mirror
• Radiation: Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.91162	1
2	0.97934	1
3	0.97892	1

• Reflection: Resolution: 1.9→29.198 Å / Num. obs: 32785 / % possible obs: 99.5 % / Redundancy: 7.1 % / B_iso Wilson estimate: 22.755 Ų / R_merge(I) obs: 0.107 / R_sym value: 0.107

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	Rsym value	% possible all
1.9-1.95	7.2	0.625	1	17160	2391	0.625	99.7
1.95-2	7.2	0.489	1.6	16705	2313	0.489	99.2
2-2.06	7.2	0.386	2	16136	2230	0.386	99.6
2.06-2.12	7.2	0.324	2.1	15843	2200	0.324	99.1
2.12-2.19	7.2	0.277	2.8	15215	2113	0.277	99.6
2.19-2.27	7.2	0.243	1.3	14911	2066	0.243	99.5
2.27-2.36	7.2	0.195	3.9	14394	2006	0.195	99.6
2.36-2.45	7.2	0.179	4.2	13767	1906	0.179	99.6
2.45-2.56	7.2	0.153	4.8	13214	1837	0.153	99.4
2.56-2.69	7.1	0.137	5.1	12773	1792	0.137	99.7
2.69-2.83	7.1	0.126	5.7	12037	1687	0.126	99.6
2.83-3	7.1	0.115	5.9	11441	1613	0.115	99.6
3-3.21	7.1	0.089	7.3	10692	1515	0.089	99.4
3.21-3.47	7	0.08	7.7	9955	1427	0.08	99.8
3.47-3.8	7	0.067	8.4	9185	1313	0.067	99.8
3.8-4.25	6.9	0.061	9.7	8355	1210	0.061	99.9
4.25-4.91	6.8	0.059	9.8	7350	1081	0.059	100
4.91-6.01	6.7	0.065	8	6188	921	0.065	99.6
6.01-8.5	6.5	0.064	9.2	4795	739	0.064	99.8
8.5-29.2	6	0.057	9.3	2536	425	0.057	96

Phasing

• Phasing: Method: MAD

Processing

Software

Name	Version	Classification	NB
REFMAC	5.2.0019	refinement
PHENIX		refinement
SHELX		phasing
MolProbity	3beta29	model building
SCALA		data scaling
PDB_EXTRACT	3.004	data extraction
MOSFLM		data reduction
SHELXD		phasing
autoSHARP		phasing

Refinement

Method to determine structure: MAD / Resolution: 1.9→29.198 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.958 / SU B: 4.585 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.106
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF ZN ION. 5. THERE ARE SOME UNINTERPRETABLE DENSITIES NEAR ZN-COORDINATING WATERS. 6. EDO MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.181	1663	5.1 %	RANDOM
Rwork	0.158	-	-	-
obs	0.16	32757	99.31 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 29.295 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.16 Å2	0.08 Å2	0 Å2
2-	-	0.16 Å2	0 Å2
3-	-	-	-0.25 Å2

Refinement step

Cycle: LAST / Resolution: 1.9→29.198 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2379	0	41	311	2731

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	2584
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	1830
X-RAY DIFFRACTION	r_angle_refined_deg	1.617	1.978	3502
X-RAY DIFFRACTION	r_angle_other_deg	1.402	3	4443
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.117	5	341
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.508	22.941	119
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.441	15	444
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.465	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	390
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2910
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	547
X-RAY DIFFRACTION	r_nbd_refined	0.181	0.2	468
X-RAY DIFFRACTION	r_nbd_other	0.146	0.2	1958
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	1214
X-RAY DIFFRACTION	r_nbtor_other	0.072	0.2	1313
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.091	0.2	269
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.155	0.2	6
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.14	0.2	59
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.127	0.2	29
X-RAY DIFFRACTION	r_mcbond_it	1.063	2	1831
X-RAY DIFFRACTION	r_mcbond_other	0.165	2	647
X-RAY DIFFRACTION	r_mcangle_it	1.546	4	2578
X-RAY DIFFRACTION	r_scbond_it	3.279	6	1053
X-RAY DIFFRACTION	r_scangle_it	4.608	8	906

LS refinement shell

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

	Rfactor	Num. reflection	% reflection
Rfree	0.274	129	-
Rwork	0.2	2262	-
all	-	2391	-
obs	-	-	99.54 %

Refinement TLS params.

Method: refined / Origin x: 80.835 Å / Origin y: 27.236 Å / Origin z: 1.533 Å

	11	12	13	21	22	23	31	32	33
T	-0.2314 Å2	-0.024 Å2	-0.0025 Å2	-	-0.1329 Å2	-0.0101 Å2	-	-	-0.1926 Å2
L	0.6216 °2	-0.2943 °2	0.032 °2	-	0.6666 °2	0.1026 °2	-	-	0.4762 °2
S	0.0324 Å °	0.1169 Å °	-0.1594 Å °	-0.0801 Å °	-0.0395 Å °	0.1023 Å °	0.0769 Å °	-0.08 Å °	0.0071 Å °