PDB-3npe: Structure of VP14 in complex with oxygen

ID or keywords:

Entry

Database: PDB / ID: 3npe

Title

Structure of VP14 in complex with oxygen

Components

9-cis-epoxycarotenoid dioxygenase 1, chloroplastic

Keywords

OXIDOREDUCTASE /

dioxygenase / seven blade beta propeller /

abscisic acid / non heme iron

Function / homology

Function and homology information

9-cis-epoxycarotenoid dioxygenase / abscisic acid biosynthetic process /

9-cis-epoxycarotenoid dioxygenase activity /

carotenoid dioxygenase activity / carotene catabolic process /

chloroplast stroma /

chloroplast /

metal ion binding
Similarity search - Function

Biological species

Zea mays (maize)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

MAD / Resolution: 3.2 Å

Authors

Messing, S.A. / Gabelli, S.B. / Amzel, L.M.

Citation

Journal: Plant Cell / Year: 2010
Title: Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid.
Authors: Messing, S.A. / Gabelli, S.B. / Echeverria, I. / Vogel, J.T. / Guan, J.C. / Tan, B.C. / Klee, H.J. / McCarty, D.R. / Amzel, L.M.

History

Deposition	Jun 28, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 10, 2010	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
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.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_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_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_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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PDBx/mmCIF format	3npe.cif.gz	223.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/3npe ftp://data.pdbj.org/pub/pdb/validation_reports/np/3npe	HTTPS FTP

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Related structure data

Similar structure data	1k4y-d 2xmd-d 4dl1-10 6et2-1 2q72-d 5z6h-2 6lf7-d 1d2v-3 6xta-d 6wy5-2 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	#147 - Mar 2012 Rhodopsin similarity (3) #66 - Jun 2005 Carotenoid Oxygenase similarity (2) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #57 - Sep 2004 Catalase similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #41 - May 2003 Hemoglobin similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #159 - Mar 2013 Erythrocruorin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#147 - Mar 2012
Rhodopsin
similarity (3)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (2)
#187 - Jul 2015
New Delhi Metallo-β-Lactamase
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#57 - Sep 2004
Catalase
similarity (1)
#111 - Mar 2009
Hydrogenase
similarity (1)
#263 - Nov 2021
Acetohydroxyacid Synthase
similarity (1)
#41 - May 2003
Hemoglobin
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#244 - Apr 2020
Photosynthetic Supercomplexes
similarity (1)
#159 - Mar 2013
Erythrocruorin
similarity (1)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#206 - Feb 2017
Globin Evolution
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#61 - Jan 2005
Phenylalanine Hydroxylase
similarity (1)
#142 - Oct 2011
PDB Pioneers
similarity (1)

Deposited unit

A: 9-cis-epoxycarotenoid dioxygenase 1, chloroplastic

hetero molecules

58 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	161.521, 161.521, 150.816
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	182
Space group name H-M	P6₃22

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Protein , 1 types, 1 molecules A

#1: Protein	9-cis-epoxycarotenoid dioxygenase 1, chloroplastic / / Protein VIVIPAROUS14 / VP-14 Mass: 57646.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: VP14 / Plasmid: pMal c2x hv / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: O24592, 9-cis-epoxycarotenoid dioxygenase

#1: Protein

9-cis-epoxycarotenoid dioxygenase 1, chloroplastic /

/ Protein VIVIPAROUS14 / VP-14

Mass: 57646.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Zea mays (maize) / Gene: VP14 / Plasmid: pMal c2x hv / Production host:

Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: O24592,

9-cis-epoxycarotenoid dioxygenase

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Non-polymers , 5 types, 16 molecules

#2: Chemical	ChemComp-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-OXY / OXYGEN MOLECULE / Oxygen Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O₂
#4: Chemical	ChemComp-OH / HYDROXIDE ION / Hydroxide Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#5: Chemical	ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₈O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 10 / 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: 4.93 Å³/Da / Density % sol: 71.64 %
Crystal grow	Temperature: 298 K / Method: hanging drop / pH: 7.5 Details: PEG 4000, Li sulfate, dioxane, 1,6 hexandiol, pH 7.5, hanging drop, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.97989 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2007

Radiation

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

Radiation wavelength

Wavelength: 0.97989 Å / Relative weight: 1

Reflection

Redundancy: 21.1 % / Av σ(I) over netI: 27.1 / Number: 293520 / R_merge(I) obs: 0.103 / Χ²: 0.88 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 13892 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
7.75	50	99.7	1	0.047	1.772	18.9
6.15	7.75	100	1	0.068	0.988	20.6
5.38	6.15	100	1	0.091	0.829	21.1
4.89	5.38	100	1	0.095	0.789	21.3
4.54	4.89	100	1	0.097	0.771	21.4
4.27	4.54	100	1	0.133	0.766	21.6
4.05	4.27	100	1	0.219	0.729	21.7
3.88	4.05	100	1	0.35	0.747	21.7
3.73	3.88	100	1	0.455	0.718	21.6
3.6	3.73	100	1	0.564	0.747	21.8

Reflection

Resolution: 3→50 Å / Num. obs: 23752 / % possible obs: 99.9 % / Redundancy: 18.5 % / R_merge(I) obs: 0.075 / Net I/σ(I): 6.7

Reflection shell

Resolution (Å)	Redundancy (%)	% possible all	R_merge(I) obs
3-3.11	10.3	99.7
3.11-3.23	14.5	99.9	0.944
3.23-3.38	18.2	99.9	0.573
3.38-3.56	20.4	99.9	0.397
3.56-3.78	20.7	100	0.24
3.78-4.07	20.7	100	0.152
4.07-4.48	20.6	100	0.08
4.48-5.13	20.5	100	0.054
5.13-6.46	20.2	100	0.047
6.46-50	18.4	99.6	0.027

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 3.8 Å / D res low: 50 Å / FOM : 0.58 / Reflection: 11806

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9537	3.67	-3.24
1	3 wavelength	2	0.979	6.55	-10.24
1	3 wavelength	3	0.9792	3.9	-9.42

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	60	0.29	0.075	0.131	0.59
2	Se	60	0.576	0.301	0.071	0.393
3	Se	60	0.333	0.153	0.087	0.793
4	Se	60	0.431	0.326	0.151	0.582
5	Se	60	0.139	0.418	0.016	0.504
6	Se	60	0.417	0.273	0.036	0.558
7	Se	60	0.41	0.243	0.032	0.725
8	Se	60	0.218	0.088	0.086	0.39

Phasing MAD shell

Resolution (Å)	FOM	Reflection
13.55-50	0.67	640
8.6-13.55	0.71	1017
6.74-8.6	0.74	1268
5.72-6.74	0.7	1457
5.05-5.72	0.65	1637
4.58-5.05	0.61	1787
4.21-4.58	0.47	1930
3.92-4.21	0.36	2070

Phasing dm

FOM : 0.59 / FOM acentric: 0.6 / FOM centric: 0.59 / Reflection: 13793 / Reflection acentric: 11437 / Reflection centric: 2356

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
10.3-46.633	0.92	0.95	0.87	686	405	281
6.4-10.3	0.85	0.88	0.78	1917	1449	468
5.1-6.4	0.77	0.79	0.67	2323	1905	418
4.5-5.1	0.71	0.72	0.63	2297	1953	344
3.9-4.5	0.51	0.52	0.42	4063	3521	542
3.6-3.9	0.19	0.19	0.16	2507	2204	303

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.03	phasing
RESOLVE	2.03	phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.2→47.3 Å / Cor.coef. F_o:F_c: 0.913 / Cor.coef. F_o:F_c free: 0.886 / Occupancy max: 1 / Occupancy min: 0.97 / SU B: 46.123 / SU ML: 0.354 / SU R Cruickshank DPI: 1.128 / Cross valid method: THROUGHOUT / ESU R: 1.004 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27164	1016	5.2 %	RANDOM
R_work	0.24066	-	-	-
obs	0.2422	18636	99.71 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 85.29 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.45 Å²	0.73 Å²	0 Å²
2-	-	1.45 Å²	0 Å²
3-	-	-	-2.18 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→47.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4010	0	22	10	4042

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	4138
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.466	1.96	5618
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.574	5	521
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.003	23.283	198
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.84	15	614
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.536	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	607
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3253
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.2	1903
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.319	0.2	2719
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	166
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.221	0.2	32
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.117	0.2	1
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.411	1.5	2647
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.671	2	4167
X-RAY DIFFRACTION	r_scbond_it	0.937	3	1639
X-RAY DIFFRACTION	r_scangle_it	1.505	4.5	1451
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.2→3.283 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.349	88	-
R_work	0.32	1318	-
obs	-	-	99.93 %

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	0.6645	-0.2026	-0.2339	5.8833	-1.8172	1.0869	-0.1031	0.7239	0.0206	-0.718	-0.2789	-0.098	-0.2189	0.2612	0.382	0.1584	-0.0037	0.2109	0.1454	-0.0944	-0.109	6.231	78.04	74.189
2	2.6331	-0.3954	-0.7038	3.1388	-0.6536	3.374	-0.3339	0.4275	-0.4439	-0.4204	-0.1294	0.1553	0.0542	-0.132	0.4633	-0.1753	-0.0205	0.4727	-0.0805	-0.2926	-0.0729	-0.12	53.716	88.305
3	8.858	-2.9202	0.1127	1.437	-2.2013	9.8745	-0.1494	-1.1902	0.9169	-2.6883	-1.4132	0.338	-2.0875	-0.3318	1.5626	0.3432	0.3048	0.2485	0.6509	0.2593	0.322	4.476	56.811	97.308

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	83 - 130
2	X-RAY DIFFRACTION	1	A	196 - 248
3	X-RAY DIFFRACTION	2	A	131 - 195
4	X-RAY DIFFRACTION	2	A	249 - 431
5	X-RAY DIFFRACTION	2	A	448 - 535
6	X-RAY DIFFRACTION	2	A	545 - 605
7	X-RAY DIFFRACTION	2	X	1 - 2
8	X-RAY DIFFRACTION	2		2946 - 2948
9	X-RAY DIFFRACTION	3	A	432 - 447
10	X-RAY DIFFRACTION	3	A	536 - 544

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