PDB-4xxf: L-fuculose 1-phosphate aldolase from Glaciozyma antarctica PI12

Basic information

• Entry: Database: PDB / ID: 4xxf
• Title: L-fuculose 1-phosphate aldolase from Glaciozyma antarctica PI12
• Components: Fuculose-1-phosphate aldolase
• Keywords: LYASE / fuculose 1-phosphate aldolase / psychrophiles / metalloenzyme

Function / homology

Function:

L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / metal ion binding

Domain/homology:

L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta

Component:

Fuculose-1-phosphate aldolase

• Biological species: Glaciozyma antarctica (fungus)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
• Authors: Jaafar, N.R. / Abu Bakar, F.D. / Abdul Murad, A.M. / Illias, R. / Littler, D. / Beddoe, T. / Rossjohn, J. / Mahadi, M.N.

Funding support

Malaysia, 1items

Organization	Grant number	Country
		Malaysia

• Citation: Journal: Acta Crystallogr.,Sect.F / Year: 2016; Title: Crystal structure of fuculose aldolase from the Antarctic psychrophilic yeast Glaciozyma antarctica PI12.; Authors: Jaafar, N.R. / Littler, D. / Beddoe, T. / Rossjohn, J. / Illias, R.M. / Mahadi, N.M. / Mackeen, M.M. / Murad, A.M. / Abu Bakar, F.D.

History

Deposition	Jan 30, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2015	Group: Data collection
Revision 1.2	Nov 16, 2016	Group: Database references
Revision 1.3	Dec 25, 2019	Group: Data collection / Database references / Derived calculations Category: citation / citation_author / diffrn_source / pdbx_struct_oper_list Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Nov 8, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

Assembly

Deposited unit

A: Fuculose-1-phosphate aldolase

hetero molecules

Summary:

• 28.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	28,237	2
Polymers	28,171	1
Non-polymers	65	1
Water	4,179	232

1

A: Fuculose-1-phosphate aldolase

hetero molecules

A: Fuculose-1-phosphate aldolase

hetero molecules

A: Fuculose-1-phosphate aldolase

hetero molecules

A: Fuculose-1-phosphate aldolase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	112,946	8
Polymers	112,685	4
Non-polymers	262	4
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-x+1,-y,z	1
crystal symmetry operation	3_545	-y+1/2,x-1/2,z	1
crystal symmetry operation	4_555	y+1/2,-x+1/2,z	1

Calculated values:

Buried area	11350 Å2
ΔGint	-224 kcal/mol
Surface area	35520 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	84.330, 84.330, 78.500
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P4212

Components on special symmetry positions

ID	Model	Components
1	1	A-473- HOH
2	1	A-619- HOH

• Details: gel filtration

Components

#1: Protein

A Fuculose-1-phosphate aldolase

Details:

Mass: 28171.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glaciozyma antarctica (fungus) / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0J9X279*PLUS, L-fuculose-phosphate aldolase

#2: Chemical

A-301 ChemComp-ZN / ZINC ION

Details:

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

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H₂O

• Sequence details: THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 2.48 ų/Da / Density % sol: 50.34 %; Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
• Crystal grow: Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 8000, magnesium chloride, Tris-HCl

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
• Detector: Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2013
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9537 Å / Relative weight: 1
• Reflection: Resolution: 1.34→37.71 Å / Num. obs: 61957 / % possible obs: 96.9 % / Redundancy: 15.7 % / B_iso Wilson estimate: 11.95 Ų / R_merge(I) obs: 0.104 / Net I/σ(I): 14.6
• Reflection shell: Resolution: 1.34→1.41 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 2 / % possible all: 81.9

Processing

Software

Name	Version	Classification
PHENIX	1.8.4	refinement
Coot		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OCR

3ocr

Resolution: 1.34→37.71 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.75 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.

	Rfactor	Num. reflection	% reflection
Rfree	0.187	3132	5.07 %
Rwork	0.1714	971734	-
obs	0.1722	61814	96.61 %

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.34→37.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1920	0	1	232	2153

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2043
X-RAY DIFFRACTION	f_angle_d	1.063	2790
X-RAY DIFFRACTION	f_dihedral_angle_d	13.799	741
X-RAY DIFFRACTION	f_chiral_restr	0.039	313
X-RAY DIFFRACTION	f_plane_restr	0.005	363

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.34-1.361	0.2169	103	0.2517	2043	X-RAY DIFFRACTION	75
1.361-1.3833	0.2577	118	0.2352	2184	X-RAY DIFFRACTION	81
1.3833-1.4071	0.2846	123	0.2323	2344	X-RAY DIFFRACTION	87
1.4071-1.4327	0.2343	158	0.233	2458	X-RAY DIFFRACTION	91
1.4327-1.4603	0.2456	157	0.2052	2627	X-RAY DIFFRACTION	97
1.4603-1.4901	0.2036	142	0.1863	2710	X-RAY DIFFRACTION	100
1.4901-1.5225	0.1746	133	0.1739	2739	X-RAY DIFFRACTION	100
1.5225-1.5579	0.1896	138	0.1569	2737	X-RAY DIFFRACTION	100
1.5579-1.5969	0.1776	149	0.152	2734	X-RAY DIFFRACTION	100
1.5969-1.64	0.1774	145	0.1547	2720	X-RAY DIFFRACTION	100
1.64-1.6883	0.146	141	0.1561	2755	X-RAY DIFFRACTION	100
1.6883-1.7428	0.1709	143	0.1622	2736	X-RAY DIFFRACTION	100
1.7428-1.8051	0.1921	157	0.1585	2739	X-RAY DIFFRACTION	100
1.8051-1.8773	0.1676	138	0.1704	2757	X-RAY DIFFRACTION	100
1.8773-1.9628	0.2472	144	0.2003	2714	X-RAY DIFFRACTION	98
1.9628-2.0663	0.1872	144	0.1623	2758	X-RAY DIFFRACTION	100
2.0663-2.1957	0.1742	150	0.1575	2763	X-RAY DIFFRACTION	100
2.1957-2.3652	0.1876	145	0.1793	2724	X-RAY DIFFRACTION	99
2.3652-2.6032	0.1909	159	0.1692	2797	X-RAY DIFFRACTION	100
2.6032-2.9797	0.1864	151	0.1787	2815	X-RAY DIFFRACTION	100
2.9797-3.7536	0.1773	150	0.1685	2847	X-RAY DIFFRACTION	100
3.7536-37.7284	0.174	144	0.1599	2981	X-RAY DIFFRACTION	98

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	3.3862	3.1454	3.1504	3.2579	2.4367	7.193	0.025	-0.2221	0.3335	-0.1415	-0.4303	0.7236	-0.0476	-0.4371	0.3862	0.1441	0.0591	0.0713	0.2246	-0.0547	0.3035	16.5421	20.2337	29.888
2	2.1977	-2.0359	-1.1048	3.0985	1.236	1.6435	-0.0058	-0.0388	0.1436	0.108	0.0083	0.0589	-0.067	-0.0995	0.0133	0.1117	0.0075	0.0118	0.0971	-0.0089	0.1251	31.3413	21.5412	30.4386
3	1.8937	-0.1918	-0.1956	1.5745	0.2326	1.8703	-0.0443	-0.0218	0.2653	-0.006	0.0788	-0.0237	-0.1708	-0.0198	-0.0383	0.1426	0.0132	0.0013	0.1321	0.0092	0.1408	36.4286	25.4535	22.3279
4	1.5156	-0.122	-0.0068	1.9026	-0.0722	1.0479	0.0009	-0.0129	0.2062	-0.0593	0.0161	0.0457	-0.1477	0.0467	-0.0087	0.1254	-0.0018	0.01	0.1074	-0.0211	0.1519	40.6588	25.8405	28.5557
5	4.6979	-2.5815	-0.079	6.2339	-1.6589	4.2295	-0.0392	0.0477	0.352	0.152	0.0865	-0.068	-0.3488	0.1521	0.0153	0.1702	-0.0455	-0.0066	0.1276	-0.0324	0.2252	44.613	32.7476	28.2604
6	1.887	0.7883	0.1695	0.4969	0.2036	1.3834	-0.1032	0.049	0.5285	-0.0278	0.0441	-0.0193	-0.2337	0.0678	0.046	0.1829	0.0057	-0.0076	0.1438	0.0312	0.2374	34.2811	28.8925	16.3695
7	2.7542	-0.249	0.2816	0.7989	0.395	0.6302	0.0121	0.1013	0.0158	-0.0872	0.0091	0.0946	-0.0341	-0.0748	-0.0235	0.1587	0.0086	-0.0184	0.1634	0.0333	0.1309	31.3658	13.5174	4.8224
8	3.9374	-3.0143	0.9719	5.9326	3.3293	9.1545	-0.0743	0.1311	0.3256	-0.3638	0.2312	-1.0914	-0.0361	1.1827	-0.1255	0.2493	0.0193	0.0391	0.297	0.0674	0.3349	36.2871	29.8706	5.5008
9	0.7879	-0.2814	-0.3833	1.099	0.578	0.9114	0.023	0.0661	0.0758	-0.0836	-0.0038	0.046	-0.0584	-0.0511	-0.0235	0.1248	0.0099	-0.006	0.122	0.0226	0.1112	32.1067	16.1055	10.4086
10	3.5184	-2.1502	0.3116	3.6979	1.8146	1.7097	0.1514	0.1733	0.0996	-0.2601	-0.2056	0.2394	-0.0704	-0.2897	0.0893	0.143	0.0042	-0.0232	0.156	0.0593	0.1661	18.8241	10.4182	4.0309
11	2.2141	0.3392	0.6814	2.1533	0.0365	2.3015	0.05	-0.151	0.0011	0.1272	0.0139	0.0401	0.0082	-0.075	-0.0677	0.1181	0.0051	0.0328	0.1036	-0.0051	0.1154	29.2151	12.9102	29.426

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 26 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 60 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 61 through 80 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 81 through 103 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 104 through 120 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 121 through 145 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 146 through 175 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 176 through 195 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 196 through 238 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 239 through 258 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 259 through 283 )