PDB-2qck: Crystal structure of flavin reductase domain protein (YP_831077.1...

Basic information

• Entry: Database: PDB / ID: 2qck
• Title: Crystal structure of flavin reductase domain protein (YP_831077.1) from Arthrobacter sp. FB24 at 1.90 A resolution
• Components: Flavin reductase domain protein
• Keywords: OXIDOREDUCTASE / YP_831077.1 / Flavin reductase domain protein / Flavin reductase like domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2

Function / homology

Function:

FMN binding

Domain/homology:

Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta

Component:

PHOSPHATE ION / Flavin reductase domain protein, FMN-binding protein

• Biological species: Arthrobacter sp. (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
• Authors: Joint Center for Structural Genomics (JCSG)
• Citation: Journal: To be published; Title: Crystal structure of flavin reductase domain protein (YP_831077.1) from Arthrobacter sp. FB24 at 1.90 A resolution; Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Jun 19, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 3, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5	Jan 25, 2023	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _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

• Remark 300: BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. CRYSTAL PACKING OF THIS STRUCTURE SUGGESTS THAT THE BIOLOGICALLY RELEVANT FORM IS A DIMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE.
• Remark 999: SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

Assembly

Deposited unit

A: Flavin reductase domain protein

hetero molecules

Summary:

• 18.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	18,699	2
Polymers	18,604	1
Non-polymers	95	1
Water	1,135	63

1

A: Flavin reductase domain protein

hetero molecules

A: Flavin reductase domain protein

hetero molecules

Summary:

• defined by author&software
• 37.4 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	37,398	4
Polymers	37,208	2
Non-polymers	190	2
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_765	-x+2,-y+1,z	1

Calculated values:

Buried area	5210 Å2
ΔGint	-43 kcal/mol
Surface area	14300 Å2
Method	PISA, PQS

2

A: Flavin reductase domain protein

hetero molecules

A: Flavin reductase domain protein

hetero molecules

A: Flavin reductase domain protein

hetero molecules

A: Flavin reductase domain protein

hetero molecules

Summary:

• defined by software
• 74.8 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	74,796	8
Polymers	74,416	4
Non-polymers	380	4
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_765	-x+2,-y+1,z	1
crystal symmetry operation	9_765	-x+2,-x+y+1,-z+1/3	1
crystal symmetry operation	12_555	x,x-y,-z+1/3	1

Calculated values:

Buried area	13640 Å2
ΔGint	-117 kcal/mol
Surface area	26120 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	60.510, 60.510, 180.700
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	180
Space group name H-M	P6222

• Details: REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN. CRYSTAL STRUCTURE PACKING REMARK 300 SUGGESTS THAT THE BIOLOGICALLY RELEVANT FORM IS A DIMER. REMARK 300 SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE. REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE DIMER REPRESENTING THE POSSIBLE REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE REMARK 350 CAN BE GENERATED BY APPLYING REMARK 350 BIOMT TRANSFORMATIONS GIVEN BELOW. REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAIN: A REMARK 350 BIOMT1 1 1.000000 -0.000000 -0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 90.76500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 52.40300 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000

Components

#1: Protein

A Flavin reductase domain protein / FMN binding domain protein

Details:

Mass: 18604.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: FB24 / Gene: YP_831077.1, Arth_1583 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0JVA7

#2: Chemical

A-167 ChemComp-PO4 / PHOSPHATE ION / Phosphate

Details:

Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄

#3: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.58 ų/Da / Density % sol: 52.26 %
• Crystal grow: Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 ; Details: NANODROP, 40.0% PEG 600, 0.1M CHES pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97908
• Detector: Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2007 / Details: Flat collimating mirror, toroid focusing mirror
• Radiation: Monochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.91162	1
2	0.97908	1

• Reflection: Resolution: 1.9→29.841 Å / Num. obs: 16301 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.73 % / B_iso Wilson estimate: 32.44 Ų / R_merge(I) obs: 0.089 / R_sym value: 0.089 / Net I/σ(I): 13.86

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Rmerge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Rsym value	% possible all
1.9-1.97	1.032	1.97	22504	2974	1.032	99.6
1.97-2.05	0.845	2.5	22545	2943	0.845	99.8
2.05-2.14	0.691	3.1	21484	2807	0.691	99.9
2.14-2.25	0.578	3.8	21922	2853	0.578	99.9
2.25-2.39	0.463	4.8	22384	2903	0.463	99.6
2.39-2.58	0.364	6.2	23079	2990	0.364	99.8
2.58-2.84	0.234	9.6	22540	2919	0.234	99.9
2.84-3.25	0.122	17.3	22581	2917	0.122	99.9
3.25-4.08	0.054	34.1	22335	2893	0.054	99.9
4.08-29.841	0.028	54.4	22467	2971	0.028	99.2

Phasing

• Phasing: Method: MAD

Processing

Software

Name	Version	Classification	NB
REFMAC	5.2.0019	refinement
PHENIX		refinement
SOLVE		phasing
MolProbity	3beta29	model building
XSCALE		data scaling
PDB_EXTRACT	3	data extraction
MAR345	CCD	data collection
XDS		data reduction

Refinement

Method to determine structure: MAD / Resolution: 1.9→29.841 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.938 / SU B: 8.645 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.142
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. RESIDUES A0-A7 ARE DISORDERED AND ARE NOT MODELED.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.251	817	5 %	RANDOM
Rwork	0.204	-	-	-
obs	0.206	16257	99.83 %	-

• 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: 30.896 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	1.1 Å2	0.55 Å2	0 Å2
2-	-	1.1 Å2	0 Å2
3-	-	-	-1.65 Å2

Refinement step

Cycle: LAST / Resolution: 1.9→29.841 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1226	0	5	63	1294

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	1292
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	852
X-RAY DIFFRACTION	r_angle_refined_deg	1.647	1.933	1767
X-RAY DIFFRACTION	r_angle_other_deg	0.981	3	2060
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.443	5	164
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.944	22.951	61
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.792	15	188
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.726	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	191
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1480
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	287
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	232
X-RAY DIFFRACTION	r_nbd_other	0.208	0.2	868
X-RAY DIFFRACTION	r_nbtor_refined	0.19	0.2	638
X-RAY DIFFRACTION	r_nbtor_other	0.092	0.2	726
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	61
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.256	0.2	34
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.307	0.2	69
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.147	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	2.44	3	859
X-RAY DIFFRACTION	r_mcbond_other	0.661	3	326
X-RAY DIFFRACTION	r_mcangle_it	3.153	5	1295
X-RAY DIFFRACTION	r_scbond_it	5.851	8	542
X-RAY DIFFRACTION	r_scangle_it	7.714	11	470

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.362	70	-
Rwork	0.328	1088	-
obs	-	1158	99.48 %

Refinement TLS params.

Method: refined / Origin x: 41.1257 Å / Origin y: 16.2239 Å / Origin z: 12.3376 Å

	11	12	13	21	22	23	31	32	33
T	-0.0395 Å2	-0.0138 Å2	-0.0382 Å2	-	-0.0737 Å2	-0.0004 Å2	-	-	-0.0167 Å2
L	0.8969 °2	0.0707 °2	-0.1521 °2	-	0.527 °2	-0.1076 °2	-	-	2.3781 °2
S	0.0454 Å °	0.034 Å °	-0.0948 Å °	-0.0441 Å °	0.0503 Å °	-0.0149 Å °	0.3932 Å °	-0.0795 Å °	-0.0958 Å °