PDB-4qpz: Crystal structure of the formolase FLS_v2 in space group P 21

ID or keywords:

Entry

Database: PDB / ID: 4qpz

Title

Crystal structure of the formolase FLS_v2 in space group P 21

Components

Formolase

Keywords

LYASE / formaldehyde lyase

Function / homology

Function and homology information

acetolactate synthase complex / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / lyase activity / magnesium ion binding
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Shen, B.W. / Siegel, J.B. / Stoddard, B.L. / Baker, D.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Computational protein design enables a novel one-carbon assimilation pathway.
Authors: Siegel, J.B. / Smith, A.L. / Poust, S. / Wargacki, A.J. / Bar-Even, A. / Louw, C. / Shen, B.W. / Eiben, C.B. / Tran, H.M. / Noor, E. / Gallaher, J.L. / Bale, J. / Yoshikuni, Y. / Gelb, M.H. ...

History

Deposition	Jun 25, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 8, 2015	Group: Database references
Revision 1.2	Sep 20, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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	4qpz.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb4qpz.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	4qpz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4qpz_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	4qpz_full_validation.pdf.gz	2.4 MB	Display
Data in XML	4qpz_validation.xml.gz	158.2 KB	Display
Data in CIF	4qpz_validation.cif.gz	208.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qp/4qpz ftp://data.pdbj.org/pub/pdb/validation_reports/qp/4qpz	HTTPS FTP

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Related structure data

Related structure data	4qq8C 2agoS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3iae-1 3iaf-d 2ag1-d 3d7k-1 2uz1-d 4qq8-d 2c31-1 7b2e-2 7ayg-2 7b2e-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) 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	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (9) #213 - Sep 2017 Sirtuins similarity (1) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

A: Formolase

B: Formolase

C: Formolase

D: Formolase

E: Formolase

F: Formolase

G: Formolase

H: Formolase

hetero molecules

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

1

A: Formolase

B: Formolase

C: Formolase

D: Formolase

hetero molecules

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

2

E: Formolase

F: Formolase

G: Formolase

H: Formolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	99.878, 136.564, 167.062
Angle α, β, γ (deg.)	90.00, 95.36, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	PHE	A	A	2 - 562	1 - 561
2	1	PHE	PHE	B	B	2 - 562	1 - 561
1	2	PHE	PHE	A	A	2 - 562	1 - 561
2	2	PHE	PHE	C	C	2 - 562	1 - 561
1	3	PHE	PHE	A	A	2 - 562	1 - 561
2	3	PHE	PHE	D	D	2 - 562	1 - 561
1	4	PHE	PHE	A	A	2 - 562	1 - 561
2	4	PHE	PHE	E	E	2 - 562	1 - 561
1	5	PHE	PHE	A	A	2 - 562	1 - 561
2	5	PHE	PHE	F	F	2 - 562	1 - 561
1	6	PHE	PHE	A	A	2 - 562	1 - 561
2	6	PHE	PHE	G	G	2 - 562	1 - 561
1	7	PHE	PHE	A	A	2 - 562	1 - 561
2	7	PHE	PHE	H	H	2 - 562	1 - 561
1	8	ALA	ALA	B	B	2 - 563	1 - 562
2	8	ALA	ALA	C	C	2 - 563	1 - 562
1	9	ALA	ALA	B	B	2 - 563	1 - 562
2	9	ALA	ALA	D	D	2 - 563	1 - 562
1	10	ALA	ALA	B	B	2 - 563	1 - 562
2	10	ALA	ALA	E	E	2 - 563	1 - 562
1	11	ALA	ALA	B	B	2 - 563	1 - 562
2	11	ALA	ALA	F	F	2 - 563	1 - 562
1	12	ALA	ALA	B	B	2 - 563	1 - 562
2	12	ALA	ALA	G	G	2 - 563	1 - 562
1	13	ALA	ALA	B	B	2 - 563	1 - 562
2	13	ALA	ALA	H	H	2 - 563	1 - 562
1	14	ALA	ALA	C	C	2 - 563	1 - 562
2	14	ALA	ALA	D	D	2 - 563	1 - 562
1	15	ALA	ALA	C	C	2 - 563	1 - 562
2	15	ALA	ALA	E	E	2 - 563	1 - 562
1	16	ALA	ALA	C	C	2 - 563	1 - 562
2	16	ALA	ALA	F	F	2 - 563	1 - 562
1	17	ALA	ALA	C	C	2 - 563	1 - 562
2	17	ALA	ALA	G	G	2 - 563	1 - 562
1	18	ALA	ALA	C	C	2 - 563	1 - 562
2	18	ALA	ALA	H	H	2 - 563	1 - 562
1	19	ALA	ALA	D	D	2 - 563	1 - 562
2	19	ALA	ALA	E	E	2 - 563	1 - 562
1	20	ALA	ALA	D	D	2 - 563	1 - 562
2	20	ALA	ALA	F	F	2 - 563	1 - 562
1	21	ALA	ALA	D	D	2 - 563	1 - 562
2	21	ALA	ALA	G	G	2 - 563	1 - 562
1	22	ALA	ALA	D	D	2 - 563	1 - 562
2	22	ALA	ALA	H	H	2 - 563	1 - 562
1	23	ALA	ALA	E	E	2 - 563	1 - 562
2	23	ALA	ALA	F	F	2 - 563	1 - 562
1	24	ALA	ALA	E	E	2 - 563	1 - 562
2	24	ALA	ALA	G	G	2 - 563	1 - 562
1	25	ALA	ALA	E	E	2 - 563	1 - 562
2	25	ALA	ALA	H	H	2 - 563	1 - 562
1	26	ALA	ALA	F	F	2 - 563	1 - 562
2	26	ALA	ALA	G	G	2 - 563	1 - 562
1	27	ALA	ALA	F	F	2 - 563	1 - 562
2	27	ALA	ALA	H	H	2 - 563	1 - 562
1	28	ALA	ALA	G	G	2 - 563	1 - 562
2	28	ALA	ALA	H	H	2 - 563	1 - 562

NCS ensembles :

#1: Protein	Formolase / Benzaldehyde lyase Mass: 61371.605 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: bznB / References: UniProt: Q9F4L3
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-TPP / THIAMINE DIPHOSPHATE Mass: 425.314 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₄O₇P₂S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.31 Å³/Da / Density % sol: 46.76 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG3350, 100 mM Succinic Acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2011

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3→166.33 Å / Num. all: 98335 / Num. obs: 89485 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / B_iso Wilson estimate: 31.46 Å² / R_sym value: 0.097 / Net I/σ(I): 10.1

Reflection shell

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique all	R_sym value	Diffraction-ID	% possible all
3-3.11	3.3	2.01	7594	0.678	1	85.4
3.11-3.23	3.4	2.96	7637	0.491	1	86

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER	MR	phasing
REFMAC	5.8.0071	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2AGO

2ago

Resolution: 3→166.33 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.898 / SU B: 60.082 / SU ML: 0.459 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.539 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25658	4028	5 %	RANDOM
R_work	0.20773	-	-	-
obs	0.21022	75975	89.43 %	-
all	-	80209	-	-

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: 67.162 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.69 Å²	0 Å²	-0.63 Å²
2-	-	4.95 Å²	0 Å²
3-	-	-	-2.11 Å²

Refinement step

Cycle: LAST / Resolution: 3→166.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	33228	0	216	11	33455

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	34140
X-RAY DIFFRACTION	r_angle_refined_deg	1.51	1.961	46597
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.94	5	4489
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.614	23.824	1360
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.942	15	5112
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.454	15	208
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	5392
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	25980
X-RAY DIFFRACTION	r_mcbond_it	1.349	3.061	17980
X-RAY DIFFRACTION	r_mcangle_it	2.284	4.593	22461
X-RAY DIFFRACTION	r_scbond_it	1.838	3.216	16160
X-RAY DIFFRACTION	r_long_range_B_refined	6.659	29.411	147112

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

LS refinement shell

Resolution: 3→3.078 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.373	306	-
R_work	0.32	5253	-
obs	-	-	83.85 %

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	1.6018	0.1035	0.4442	0.5748	0.0541	1.9621	-0.0518	-0.6411	-0.1315	0.2426	-0.0927	0.0051	-0.1396	0.0044	0.1444	0.2552	-0.0188	-0.0135	0.3136	0.1409	0.1789	5.5043	17.8514	-16.2
2	1.8197	0.3123	-0.0794	1.1958	-0.0408	2.719	-0.0251	-0.2836	-0.5675	0.0181	-0.0825	0.1744	0.4169	-0.7567	0.1076	0.1304	-0.1125	0.0203	0.2653	0.0451	0.3004	-22.8603	9.3675	-38.217
3	1.6348	-0.3871	0.4326	0.7564	-0.4423	2.4136	0.1439	0.6058	-0.194	-0.1809	-0.2814	-0.0477	-0.0279	0.3844	0.1376	0.1637	0.0641	0.006	0.2784	-0.0853	0.1707	2.0379	18.0017	-70.4939
4	2.0077	-0.8226	0.2518	1.362	-0.3946	2.2317	0.0414	0.3068	-0.4597	-0.0208	-0.2425	-0.1606	0.2729	0.976	0.2011	0.117	0.0648	0.0123	0.5022	0.0754	0.3145	30.6076	10.0621	-48.5328
5	1.6776	0.0229	0.4704	1.0712	-0.2102	2.4752	-0.0492	0.1159	0.4667	0.0296	-0.1791	-0.3861	-0.155	1.0293	0.2282	0.0624	-0.0147	-0.0217	0.4939	0.0847	0.3767	-19.0988	78.8968	-35.3892
6	1.7276	0.0474	0.4393	0.999	-0.5522	2.8168	0.0467	-0.6082	0.0403	0.2244	-0.1006	0.0762	0.2376	-0.2061	0.0538	0.173	-0.0035	0.0036	0.3235	-0.1369	0.1537	-47.001	71.3474	-12.5327
7	1.6399	-0.1855	0.5124	1.1932	-0.4089	3.2366	-0.07	-0.3792	0.4355	0.1238	0.1173	0.2865	-0.2167	-1.0148	-0.0473	0.0234	0.0719	0.0239	0.3542	-0.037	0.2837	-72.731	79.7826	-44.3049
8	1.7735	-0.1571	0.5089	1.0589	0.1652	2.8885	0.031	0.3521	0.0559	-0.1974	-0.1009	-0.1398	0.5066	0.4156	0.0699	0.1502	0.0927	0.0611	0.1429	0.0906	0.1505	-45.1612	70.9265	-67.0139

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 564
2	X-RAY DIFFRACTION	1	A	601 - 602
3	X-RAY DIFFRACTION	2	B	2 - 563
4	X-RAY DIFFRACTION	2	B	601 - 602
5	X-RAY DIFFRACTION	3	C	2 - 563
6	X-RAY DIFFRACTION	3	C	601 - 602
7	X-RAY DIFFRACTION	4	D	2 - 563
8	X-RAY DIFFRACTION	4	D	601 - 602
9	X-RAY DIFFRACTION	5	E	2 - 563
10	X-RAY DIFFRACTION	5	E	601 - 602
11	X-RAY DIFFRACTION	6	F	2 - 563
12	X-RAY DIFFRACTION	6	F	601 - 602
13	X-RAY DIFFRACTION	7	G	2 - 563
14	X-RAY DIFFRACTION	7	G	601 - 602
15	X-RAY DIFFRACTION	8	H	2 - 563
16	X-RAY DIFFRACTION	8	H	601 - 602

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