PDB-3qm3: 1.85 Angstrom Resolution Crystal Structure of Fructose-bisphospha...

ID or keywords:

Entry

Database: PDB / ID: 3qm3

Title

1.85 Angstrom Resolution Crystal Structure of Fructose-bisphosphate Aldolase (Fba) from Campylobacter jejuni

Components

Fructose-bisphosphate aldolase

Keywords

LYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TIM beta/alpha-barrel

Function / homology

Function and homology information

fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / gluconeogenesis / zinc ion binding / cytosol
Similarity search - Function

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: 1.85 Angstrom Resolution Crystal Structure of Fructose-bisphosphate Aldolase (Fba) from Campylobacter jejuni
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Feb 3, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _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	3qm3.cif.gz	1.1 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	3qm3_validation.pdf.gz	533.9 KB	Display	wwPDB validaton report
Full document	3qm3_full_validation.pdf.gz	549.5 KB	Display
Data in XML	3qm3_validation.xml.gz	133.2 KB	Display
Data in CIF	3qm3_validation.cif.gz	200.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qm/3qm3 ftp://data.pdbj.org/pub/pdb/validation_reports/qm/3qm3	HTTPS FTP

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Related structure data

Related structure data	1dosS S: Starting model for refinement
Similar structure data	3fg1-3 3v99-1 2p0m-1 3fg1-2 1lox-d 3v92-1 3s3k-d 3v98-2 6j11-3 4a22-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	TargetDB: IDP90687

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (6)

Deposited unit

A: Fructose-bisphosphate aldolase

B: Fructose-bisphosphate aldolase

C: Fructose-bisphosphate aldolase

D: Fructose-bisphosphate aldolase

E: Fructose-bisphosphate aldolase

F: Fructose-bisphosphate aldolase

G: Fructose-bisphosphate aldolase

H: Fructose-bisphosphate aldolase

hetero molecules

316 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fructose-bisphosphate aldolase

B: Fructose-bisphosphate aldolase

hetero molecules

defined by author&software
78.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Fructose-bisphosphate aldolase

D: Fructose-bisphosphate aldolase

hetero molecules

defined by author&software
78.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Fructose-bisphosphate aldolase

F: Fructose-bisphosphate aldolase

hetero molecules

defined by author&software
78.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Fructose-bisphosphate aldolase

H: Fructose-bisphosphate aldolase

hetero molecules

defined by author&software
78.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.996, 101.971, 105.662
Angle α, β, γ (deg.)	113.27, 95.34, 95.75
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Fructose-bisphosphate aldolase / FBP aldolase / FBPA / Fructose-1 / 6-bisphosphate aldolase Mass: 39048.020 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: Cj0597, fba, fda, fdaC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): KRXpGro7 / References: UniProt: Q0PAS0, fructose-bisphosphate aldolase

#1: Protein

Fructose-bisphosphate aldolase / FBP aldolase / FBPA / Fructose-1 / 6-bisphosphate aldolase

Mass: 39048.020 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: Cj0597, fba, fda, fdaC / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): KRXpGro7 / References: UniProt: Q0PAS0, fructose-bisphosphate aldolase

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Non-polymers , 6 types, 3602 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3562 / 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: 2.4 Å³/Da / Density % sol: 48.79 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5) Screen solution: 0.2M NH4 Sulfate, 0.1M Na Cacodylate pH 7.5, 30%PEG 2K MME, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97934 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2010 / Details: Mirrors
Radiation	Monochromator: Si {1,1,1} Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 1.85→30 Å / Num. all: 242214 / Num. obs: 242214 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / B_iso Wilson estimate: 17.8 Å² / R_merge(I) obs: 0.092 / Net I/σ(I): 21
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 7 % / R_merge(I) obs: 0.571 / Mean I/σ(I) obs: 3.7 / Num. unique all: 12007 / % possible all: 96.4

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHENIX		model building
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DOS

1dos

Resolution: 1.85→29.66 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.948 / SU B: 5.314 / SU ML: 0.074
Isotropic thermal model: Atomic Temperature Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19088	12186	5 %	RANDOM
R_work	0.14888	-	-	-
all	0.15097	229995	-	-
obs	0.15097	229995	97.6 %	-

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: 21.314 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.41 Å²	-0.67 Å²	-0.2 Å²
2-	-	0.64 Å²	0.98 Å²
3-	-	-	-0.44 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→29.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21314	0	159	3562	25035

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	22243
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	14875
X-RAY DIFFRACTION	r_angle_refined_deg	1.322	1.966	30090
X-RAY DIFFRACTION	r_angle_other_deg	0.844	3	36627
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.974	5	2828
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.636	25.853	991
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.538	15	3905
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.065	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	3281
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	24968
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4156
X-RAY DIFFRACTION	r_mcbond_it	0.989	1.5	13919
X-RAY DIFFRACTION	r_mcbond_other	0.342	1.5	5774
X-RAY DIFFRACTION	r_mcangle_it	1.618	2	22277
X-RAY DIFFRACTION	r_scbond_it	2.808	3	8324
X-RAY DIFFRACTION	r_scangle_it	4.342	4.5	7812

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.266	900	-
R_work	0.203	16469	-
obs	-	16469	94.81 %

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	0.6061	0.1222	-0.1443	0.7471	0.0402	0.326	0.025	-0.0555	0.0091	0.1163	-0.0439	-0.0111	-0.0117	0.031	0.0189	0.0513	-0.0142	-0.0078	0.0349	-0.0084	0.0072	55.9758	47.5155	104.3828
2	1.1531	0.4951	-0.3634	1.4033	-0.495	1.3949	0.0559	0.0614	0.2265	-0.0133	0.0178	0.0678	-0.0862	0.0011	-0.0737	0.0377	-0.0107	0.0104	0.0267	-0.003	0.0604	55.3278	65.9768	96.6642
3	0.31	-0.0726	-0.1109	1.4596	0.2536	0.2056	-0.006	0.0727	-0.0171	-0.0394	0.037	-0.1314	0.025	0.0184	-0.031	0.0123	-0.0024	-0.0002	0.042	-0.012	0.0157	68.3042	35.7733	86.728
4	1.2331	0.2541	0.1642	1.0903	-0.1845	0.9167	0.0389	-0.1045	-0.2099	0.1338	-0.0551	-0.0628	0.0664	0.0269	0.0162	0.0383	0.0012	-0.0023	0.0218	0.0207	0.0385	57.2229	15.3429	108.1249
5	2.6781	0.2768	0.8456	1.7574	0.2942	2.8214	0.1671	0.0953	-0.6987	-0.062	-0.0525	-0.1137	0.4912	0.0856	-0.1146	0.1745	0.0147	-0.0138	0.0179	0.0078	0.2698	56.1855	-2.5284	105.1323
6	0.792	0.487	-0.4132	0.8464	-0.3067	0.7769	-0.0751	0.1836	0.0169	-0.1866	0.1019	0.0742	0.0229	-0.0946	-0.0268	0.0472	-0.0058	-0.0215	0.0752	-0.0117	0.0183	53.795	27.9335	83.1833
7	0.6885	0.1211	0.0781	0.9559	-0.039	0.468	-0.0009	-0.0384	0.0165	0.0641	0.0138	-0.021	-0.0159	0.0135	-0.0129	0.015	0.0058	-0.0068	0.032	-0.021	0.0147	71.6988	16.3537	55.672
8	0.9377	0.1935	-0.2707	1.1301	-0.3359	0.6825	-0.0069	0.0975	0.1906	-0.0095	0.0758	0.0948	-0.0599	-0.0671	-0.0689	0.0247	0.0052	-0.0178	0.0446	-0.0058	0.078	62.2105	32.6391	51.1055
9	0.2898	0.0227	-0.026	0.8866	0.2652	0.2876	-0.0002	0.0561	-0.0115	-0.0355	0.0314	-0.095	0.0279	0.0367	-0.0312	0.0173	0.0027	-0.0014	0.0437	-0.0203	0.0225	78.3784	6.1359	39.5618
10	0.8566	0.2827	0.1329	0.783	0.0016	0.7058	0.0099	-0.1201	-0.0528	0.0579	0.0023	0.0575	0.0459	-0.0637	-0.0122	0.0218	0.0004	-0.0019	0.0409	0.0036	0.0182	61.4646	-8.9165	58.1635
11	1.0634	0.6319	0.5635	2.4191	-0.4356	1.876	0.098	-0.0537	-0.2279	0.0123	-0.063	-0.2437	0.292	0.1158	-0.035	0.078	0.0253	-0.0192	0.0455	0.0318	0.0678	70.333	-24.2828	64.9636
12	0.3137	0.1913	-0.2017	0.5641	-0.3571	0.9746	-0.0275	0.0565	-0.0239	-0.1135	0.0602	0.0332	0.0825	-0.0697	-0.0326	0.0279	-0.0015	-0.0159	0.0417	-0.0221	0.0231	63.2805	-5.8324	38.6646
13	0.9507	-0.3358	0.0635	1.0729	-0.0338	0.2978	0.0759	0.1024	-0.0751	-0.1026	-0.0732	0.0797	0.0533	0.0409	-0.0027	0.0271	0.0344	-0.0102	0.0822	-0.0128	0.0091	26.8408	-4.9683	35.2344
14	1.9898	-0.9457	-0.1812	2.7155	-0.6354	2.0161	0.0128	-0.1111	-0.2034	0.1642	0.0285	0.0793	0.0751	0.0679	-0.0413	0.0329	0.0297	-0.0064	0.0885	0.004	0.0558	31.4272	-18.1944	45.1036
15	0.4362	-0.1742	0.0741	1.299	0.1465	0.3212	-0.011	-0.0349	0.085	0.1069	0.0052	-0.1278	-0.0093	0.0563	0.0059	0.0126	0.002	-0.0129	0.0909	0.01	0.038	39.7454	12.7316	49.9849
16	0.6692	-0.3896	-0.4031	1.2316	-0.3649	1.2863	0.117	0.0879	0.1944	-0.1265	-0.1002	-0.1586	-0.1886	0.0798	-0.0168	0.0582	-0.0082	0.0209	0.0972	0.056	0.0926	27.8493	36.808	26.803
17	5.3017	-1.3554	-3.161	4.3915	0.4164	1.9485	0.2823	-0.7094	0.3737	0.498	-0.0684	-0.2887	-0.3073	0.4739	-0.214	0.3507	-0.0959	-0.0094	0.2718	-0.0037	0.1989	23.6722	45.7897	39.4183
18	0.5808	-0.3338	0.466	0.9119	-0.1588	0.9844	-0.0297	-0.0684	0.0479	0.245	0.0239	0.0307	0.0089	-0.0418	0.0058	0.0749	-0.0137	0.0155	0.129	0.0059	0.0539	25.3615	20.7684	53.2033
19	0.5614	-0.1775	0.1104	0.6262	-0.0836	0.2416	0.0035	0.0476	-0.0173	-0.084	-0.0123	0.0403	0.041	0.028	0.0088	0.0291	0.0006	-0.0005	0.0247	-0.0138	0.0139	17.2135	28.5742	80.6433
20	1.5086	-0.4657	0.029	2.19	-0.3448	1.6701	0.0034	-0.1062	-0.2803	0.0332	0.0841	0.1182	0.1419	0.0058	-0.0875	0.0295	0.0055	0.0012	0.0235	0.0062	0.0777	17.8307	9.8996	89.885
21	0.424	-0.0676	0.0192	1.1603	0.1924	0.2909	-0.0111	-0.0792	0.0519	0.0746	0.0157	-0.0845	-0.0318	0.0377	-0.0046	0.0154	-0.0002	-0.0092	0.0349	-0.0159	0.0152	29.645	41.3362	98.334
22	0.9776	-0.4206	-0.064	1.4729	-0.0599	0.8427	0.0644	0.1061	0.1296	-0.1037	-0.0532	0.0705	-0.0611	-0.05	-0.0112	0.0186	0.0044	0.0009	0.0213	0.0127	0.03	13.0628	57.7518	80.4686
23	2.1063	-0.6801	-0.9904	1.934	0.0422	1.9645	0.2784	0.0938	0.5678	-0.1246	-0.0928	-0.348	-0.3375	0.0729	-0.1855	0.1147	-0.018	0.0703	0.0436	0.0698	0.221	21.8275	73.3737	75.4641
24	0.6227	-0.4944	0.2067	1.2341	-0.3864	0.844	-0.0373	-0.1061	0.062	0.2079	0.0649	0.056	-0.0409	-0.038	-0.0276	0.0469	-0.0101	0.0227	0.0462	-0.0286	0.0346	14.8492	52.0399	100.1371

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 157
2	X-RAY DIFFRACTION	2	A	158 - 266
3	X-RAY DIFFRACTION	3	A	267 - 354
4	X-RAY DIFFRACTION	4	B	0 - 188
5	X-RAY DIFFRACTION	5	B	189 - 281
6	X-RAY DIFFRACTION	6	B	282 - 354
7	X-RAY DIFFRACTION	7	C	0 - 104
8	X-RAY DIFFRACTION	8	C	105 - 266
9	X-RAY DIFFRACTION	9	C	267 - 354
10	X-RAY DIFFRACTION	10	D	0 - 104
11	X-RAY DIFFRACTION	11	D	105 - 266
12	X-RAY DIFFRACTION	12	D	267 - 354
13	X-RAY DIFFRACTION	13	E	0 - 220
14	X-RAY DIFFRACTION	14	E	221 - 266
15	X-RAY DIFFRACTION	15	E	267 - 354
16	X-RAY DIFFRACTION	16	F	-2 - 260
17	X-RAY DIFFRACTION	17	F	261 - 282
18	X-RAY DIFFRACTION	18	F	283 - 354
19	X-RAY DIFFRACTION	19	G	0 - 174
20	X-RAY DIFFRACTION	20	G	175 - 266
21	X-RAY DIFFRACTION	21	G	267 - 354
22	X-RAY DIFFRACTION	22	H	0 - 104
23	X-RAY DIFFRACTION	23	H	105 - 270
24	X-RAY DIFFRACTION	24	H	271 - 354

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