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- PDB-2r6v: Crystal structure of FMN-binding protein (NP_142786.1) from Pyroc... -

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Basic information

Entry
Database: PDB / ID: 2r6v
TitleCrystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii at 1.35 A resolution
ComponentsUncharacterized protein PH0856
KeywordsFLAVOPROTEIN / NP_142786.1 / FMN-binding protein / Flavin reductase like domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


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
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NICOTINAMIDE / Uncharacterized protein PH0856
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._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 1.4Jan 25, 2023Group: 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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein PH0856
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5664
Polymers21,9261
Non-polymers6413
Water3,747208
1
A: Uncharacterized protein PH0856
hetero molecules

A: Uncharacterized protein PH0856
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1328
Polymers43,8512
Non-polymers1,2816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.200, 46.200, 267.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-183-

HOH

21A-269-

HOH

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Components

#1: Protein Uncharacterized protein PH0856


Mass: 21925.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: NP_142786.1, PH0856 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: O58586
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.57 %
Description: THE HIGH RESOLUTION DATA FROM THE PEAK WAVELENGTH IS INCOMPLETE. LOWER RESOLUTION DATA FROM THE INFLECTION AND HIGH ENERGY REMOTE WAVELENGTHS WERE MERGED WITH THE PEAK DATA TO INCREASE ...Description: THE HIGH RESOLUTION DATA FROM THE PEAK WAVELENGTH IS INCOMPLETE. LOWER RESOLUTION DATA FROM THE INFLECTION AND HIGH ENERGY REMOTE WAVELENGTHS WERE MERGED WITH THE PEAK DATA TO INCREASE THE COMPLETENESS TO 1.4 A. THIS DATA WAS USED FOR REFINEMENT AND THE STATISTICS ABOVE ARE FROM THIS MERGED DATA SET.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: NANODROP, 0.2M Ammonium formate, 20.0% PEG 3350, No Buffer pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97939, 0.97910
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979391
30.97911
ReflectionResolution: 1.25→44.588 Å / Num. obs: 41184 / % possible obs: 84.5 % / Redundancy: 18.3 % / Biso Wilson estimate: 15.957 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 23.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.25-1.293.30.3183.23995119728.2
1.29-1.355.10.2764.515904309556.6
1.35-1.415.80.2385.417396299965.3
1.41-1.487.90.196833694424894.4
1.48-1.5712.40.15912.557640466199.9
1.57-1.7200.13120.2102653514099.9
1.7-1.8725.50.10429.8121364475899.9
1.87-2.1426.30.08236.6127609485399.9
2.14-2.6926.60.072411308144921100
2.69-44.6270.05844143198531299.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.25→44.588 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.236 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.045
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 ...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 0.80 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO IS FROM CRYO CONDITION. FMN IS ASSIGNED BASED ON DENSITY, STRUCTURAL HOMOLOGS AS WELL AS INTERACTION WITH PROTEIN. NCA (NICOTINAMIDE) IS TENTATIVELY ASSIGNED BASED ON DENSITY AND INTERACTION. NCA COULD BE A PORTION OF THE PUTATIVE LIGAND NADP+ (PDB 1I0S) OR OTHER RELATED COMPOUNDS. 4. DUE TO LOW COMPLETENESS OF THE HIGH RESOLUTION DATA FROM THE PEAK WAVELENGTH, REFINEMENT WAS AGAINST DATA MERGED FROM ALL THREE WAVELENGTHS. THIS MERGED DATA IS 85 % COMPLETE OVERALL. THE NOMINAL RESOLUTION IS 1.35A WITH 4292 OBSERVED REFLECTIONS BETWEEN 1.35-1.25A (44 % COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.154 2082 5.1 %RANDOM
Rwork0.127 ---
all0.128 ---
obs0.128 41182 84.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.524 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.29 Å20 Å2
2--0.58 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.25→44.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 44 208 1696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221754
X-RAY DIFFRACTIONr_bond_other_d0.0050.021210
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9782421
X-RAY DIFFRACTIONr_angle_other_deg1.08332969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34923.24374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53315306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.425159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021973
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02376
X-RAY DIFFRACTIONr_nbd_refined0.2110.2296
X-RAY DIFFRACTIONr_nbd_other0.2060.21246
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2824
X-RAY DIFFRACTIONr_nbtor_other0.0910.2904
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.236
X-RAY DIFFRACTIONr_mcbond_it2.89531097
X-RAY DIFFRACTIONr_mcbond_other2.0773408
X-RAY DIFFRACTIONr_mcangle_it3.55251698
X-RAY DIFFRACTIONr_scbond_it4.5168846
X-RAY DIFFRACTIONr_scangle_it5.45811700
X-RAY DIFFRACTIONr_rigid_bond_restr2.84333459
X-RAY DIFFRACTIONr_sphericity_free10.3883212
X-RAY DIFFRACTIONr_sphericity_bonded4.92332891
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 52 -
Rwork0.22 834 -
obs-886 25.41 %

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