PDB-3gyr: Structure of Phenoxazinone synthase from Streptomyces antibioticu...

ID or keywords:

Entry

Database: PDB / ID: 3gyr

Title

Structure of Phenoxazinone synthase from Streptomyces antibioticus reveals a new type 2 copper center.

Components

Phenoxazinone synthase

Keywords

OXIDOREDUCTASE / METALLOPROTEIN / LACCASE / MULTICOPPER OXIDASE / HEXAMER / Antibiotic biosynthesis / Metal-binding

Function / homology

Function and homology information

o-aminophenol oxidase / o-aminophenol oxidase activity / antibiotic biosynthetic process / copper ion binding
Similarity search - Function

Biological species

Streptomyces antibioticus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Smith, A.W. / Camara-Artigas, A. / Wang, M. / Francisco, W.A. / Allen, J.P.

Citation

Journal: Biochemistry / Year: 2006
Title: Structure of Phenoxazinone Synthase from Streptomyces Antibioticus Reveals a New Type 2 Copper Center.
Authors: Smith, A.W. / Camara-Artigas, A. / Wang, M. / Allen, J.P. / Francisco, W.A.

History

Deposition	Apr 5, 2009	Deposition site: RCSB / Processing site: RCSB
Supersession	Apr 28, 2009	ID: 2G23
Revision 1.0	Apr 28, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.2	Apr 4, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3	Jul 24, 2019	Group: Data collection / Refinement description / Category: software Item: _software.classification / _software.name / _software.version
Revision 1.4	Oct 13, 2021	Group: Database references / Derived calculations / Category: database_2 / 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 / _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	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3gyr.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb3gyr.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	3gyr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3gyr_validation.pdf.gz	585.4 KB	Display	wwPDB validaton report
Full document	3gyr_full_validation.pdf.gz	688.1 KB	Display
Data in XML	3gyr_validation.xml.gz	289.2 KB	Display
Data in CIF	3gyr_validation.cif.gz	414.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gy/3gyr ftp://data.pdbj.org/pub/pdb/validation_reports/gy/3gyr	HTTPS FTP

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Related structure data

Related structure data	1gskS S: Starting model for refinement
Similar structure data	3w1i-d 3w1j-d 3jqo-d 3zbi-d 1gvh-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) 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

Related structure data

1gskS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phenoxazinone synthase

B: Phenoxazinone synthase

C: Phenoxazinone synthase

D: Phenoxazinone synthase

E: Phenoxazinone synthase

F: Phenoxazinone synthase

G: Phenoxazinone synthase

H: Phenoxazinone synthase

I: Phenoxazinone synthase

J: Phenoxazinone synthase

K: Phenoxazinone synthase

L: Phenoxazinone synthase

hetero molecules

810 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phenoxazinone synthase

B: Phenoxazinone synthase

C: Phenoxazinone synthase

D: Phenoxazinone synthase

E: Phenoxazinone synthase

F: Phenoxazinone synthase

hetero molecules

defined by author
405 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Phenoxazinone synthase

H: Phenoxazinone synthase

I: Phenoxazinone synthase

J: Phenoxazinone synthase

K: Phenoxazinone synthase

L: Phenoxazinone synthase

hetero molecules

defined by author
405 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

F: Phenoxazinone synthase

J: Phenoxazinone synthase

hetero molecules

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

4

E: Phenoxazinone synthase

K: Phenoxazinone synthase

hetero molecules

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

5

A: Phenoxazinone synthase

I: Phenoxazinone synthase

hetero molecules

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

6

B: Phenoxazinone synthase

H: Phenoxazinone synthase

hetero molecules

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

7

C: Phenoxazinone synthase

G: Phenoxazinone synthase

hetero molecules

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

8

D: Phenoxazinone synthase

L: Phenoxazinone synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	109.494, 163.456, 164.352
Angle α, β, γ (deg.)	117.04, 95.74, 107.23
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	3 - 1005
2	1	1	5	B	3 - 1005
3	1	1	5	C	3 - 1005
4	1	1	5	D	3 - 1005
5	1	1	5	E	3 - 1005
6	1	1	5	F	3 - 1005
7	1	1	5	G	3 - 1005
8	1	1	5	H	3 - 1005
9	1	1	5	I	3 - 1005
10	1	1	5	J	3 - 1005
11	1	1	5	K	3 - 1005
12	1	1	5	L	3 - 1005

#1: Protein	Phenoxazinone synthase / PHS Mass: 67094.086 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: phsA / Production host: STREPTOMYCES LIVIDANS (bacteria) / References: UniProt: Q53692, Oxidoreductases
#2: Chemical	... ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-C2O / CU-O-CU LINKAGE Mass: 143.091 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu₂O
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4377 / 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: 3.13 Å³/Da / Density % sol: 60.46 %
Crystal grow	Temperature: 278 K / pH: 5 Details: PEG 4000, SODIUM CITRATE, 2- PROPANOL, GLYCEROL, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K, PH 5.00, temperature 278K

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 2003 / Details: MIRRORS
Radiation	Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.3→55.4 Å / Num. obs: 357511 / % possible obs: 86.3 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / B_iso Wilson estimate: 36.49 Å² / R_merge(I) obs: 0.082 / R_sym value: 0.058 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2.3→2.41 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 2.6 / R_sym value: 0.28 / % possible all: 72.4

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0072	refinement
CNS		refinement
CrystalClear		data collection
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSK

1gsk

Resolution: 2.3→20 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.92 / SU B: 12.531 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22237	17920	5 %	RANDOM
R_work	0.16453	-	-	-
obs	0.16743	339025	86.34 %	-

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: 27.202 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.15 Å²	-0.02 Å²	-0.03 Å²
2-	-	0.03 Å²	0.15 Å²
3-	-	-	0.24 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	54720	0	144	4377	59241

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	56448
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.585	1.966	77148
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.089	5	7020
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.007	23.108	2664
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.281	15	8280
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.079	15	516
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	8196
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.022	44916
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.982	2	35160
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.034	3	56952
X-RAY DIFFRACTION	r_scbond_it	2.402	2	21288
X-RAY DIFFRACTION	r_scangle_it	3.402	3	20196
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	2348	medium positional	0.2	0.5
B	2348	medium positional	0.15	0.5
C	2348	medium positional	0.15	0.5
D	2348	medium positional	0.25	0.5
E	2348	medium positional	0.17	0.5
F	2348	medium positional	0.14	0.5
G	2348	medium positional	0.15	0.5
H	2348	medium positional	0.17	0.5
I	2348	medium positional	0.21	0.5
J	2348	medium positional	0.17	0.5
K	2348	medium positional	0.14	0.5
L	2348	medium positional	0.15	0.5
A	2218	loose positional	0.38	5
B	2218	loose positional	0.37	5
C	2218	loose positional	0.35	5
D	2218	loose positional	0.48	5
E	2218	loose positional	0.43	5
F	2218	loose positional	0.39	5
G	2218	loose positional	0.35	5
H	2218	loose positional	0.38	5
I	2218	loose positional	0.53	5
J	2218	loose positional	0.38	5
K	2218	loose positional	0.4	5
L	2218	loose positional	0.37	5
A	2348	medium thermal	3.11	2
B	2348	medium thermal	2.3	2
C	2348	medium thermal	2.87	2
D	2348	medium thermal	4	2
E	2348	medium thermal	2.37	2
F	2348	medium thermal	2.15	2
G	2348	medium thermal	2.22	2
H	2348	medium thermal	2.93	2
I	2348	medium thermal	4.14	2
J	2348	medium thermal	3.39	2
K	2348	medium thermal	2.47	2
L	2348	medium thermal	2.5	2
A	2218	loose thermal	3.23	10
B	2218	loose thermal	2.56	10
C	2218	loose thermal	2.98	10
D	2218	loose thermal	3.82	10
E	2218	loose thermal	2.69	10
F	2218	loose thermal	2.55	10
G	2218	loose thermal	2.6	10
H	2218	loose thermal	2.96	10
I	2218	loose thermal	4.03	10
J	2218	loose thermal	3.51	10
K	2218	loose thermal	2.82	10
L	2218	loose thermal	2.68	10

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.335	1179	-
R_work	0.256	20417	-
obs	-	-	71.35 %

Refinement TLS params.

L11: 0 °² / L12: 0 °² / L13: 0 °² / L22: 0 °² / L23: 0 °² / L33: 0 °² / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å² / T12: 0 Å² / T13: 0 Å² / T22: 0 Å² / T23: 0 Å² / T33: 0 Å² / Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	-0.6581	-43.4537	34.9318
2	-0.5185	8.2022	55.0949
3	-0.7333	51.5114	20.6155
4	-0.8814	43.4871	-34.3611
5	-0.7448	-8.1566	-54.2366
6	-0.7449	-51.4022	-19.7927
7	44.0977	51.6293	20.2105
8	44.346	8.3303	55.0513
9	44.2907	-43.3341	34.9134
10	44.1194	-51.5163	-19.8062
11	44.0846	-8.3659	-54.2964
12	44.0292	43.3267	-34.4656

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	37 - 628
2	X-RAY DIFFRACTION	2	B	37 - 628
3	X-RAY DIFFRACTION	3	C	37 - 628
4	X-RAY DIFFRACTION	4	D	37 - 628
5	X-RAY DIFFRACTION	5	E	37 - 628
6	X-RAY DIFFRACTION	6	F	37 - 628
7	X-RAY DIFFRACTION	7	G	37 - 628
8	X-RAY DIFFRACTION	8	H	37 - 628
9	X-RAY DIFFRACTION	9	I	37 - 628
10	X-RAY DIFFRACTION	10	J	37 - 628
11	X-RAY DIFFRACTION	11	K	37 - 628
12	X-RAY DIFFRACTION	12	L	37 - 628

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