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- PDB-3ge5: Crystal structure of a putative nad(p)h:fmn oxidoreductase (pg031... -

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Basic information

Entry
Database: PDB / ID: 3ge5
TitleCrystal structure of a putative nad(p)h:fmn oxidoreductase (pg0310) from porphyromonas gingivalis w83 at 1.70 A resolution
Componentsputative NAD(P)H:FMN oxidoreductase
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Unknown ligand / Nitroreductase family protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis W83 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative NAD(P)H:FMN oxidoreductase (NP_904626.1) from PORPHYROMONAS GINGIVALIS W83 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 1.4Feb 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative NAD(P)H:FMN oxidoreductase
B: putative NAD(P)H:FMN oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,83614
Polymers46,3252
Non-polymers1,51112
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-56 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.060, 112.060, 68.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-196-

HOH

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein putative NAD(P)H:FMN oxidoreductase / Nitroreductase family protein


Mass: 23162.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis W83 (bacteria)
Gene: NP_904626.1, PG_0310 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7MX99

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Non-polymers , 5 types, 501 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.31 Å3/Da / Density % sol: 46.85 %
Description: THE AND R MERGE VALUES REPORTED HERE ARE BASED ON TREATING FRIEDEL PAIRS AS SEPARATE REFLECTIONS.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.0000M (NH4)2SO4, 0.1M TRIS pH 8.5, NANODROP, 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: 0.91837,0.97870,0.97833
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 14, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97871
30.978331
ReflectionResolution: 1.7→29.161 Å / Num. obs: 48232 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.057 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.760.7351.8313078862198
1.76-1.830.552.5328719056199.7
1.83-1.910.3823.6325428795199.5
1.91-2.020.2565.4372559923199.7
2.02-2.140.1787.7331238665199.7
2.14-2.310.12710.4357239329199.7
2.31-2.540.08714.8348899054199.7
2.54-2.90.06219.8345558950199.8
2.9-3.660.03233.1359829278199.8
3.66-29.1610.02247.7355369139199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.161 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.841 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.082
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. A FLAVIN MONONUCLEOTIDE (FMN) MOLECULE ARE MODELED INTO THE PUTATIVE ACTIVE SITE ON EACH MONOMER. DURING THE REFINEMENT, THE FMN RESTRAINTS DICTIONARY WAS MODIFIED TO ALLOW BENDING OF THE ISOALLOXAZINE RING ALONG THE N5-N10 VIRTUAL AXIS RESULTING IN AN IMPROVED FIT BETWEEN THE FNN COORDINATES AND ELECTRON DENSITY. 5. AN UNKNOWN LIGAND (UNL) MOLECULE IS MODELED INTO THE PUTATIVE ACTIVE SITE OF EACH MONOMER. EACH UNL IS LOCATED ABOVE THE ISOALLOXAZINE MOIETY OF EACH FMN AND ITS SHAPE IS SIMILAR TO EITHER BENZOATE/NITOBENZENE OR BENZOATE/NITROBENZENE DERIVATIVES. 6. SULFATE (SO4) ION AND ETHYLENE GLYCOL (EDO) ARE MODELED BASED ON CRYSTALLIZATION AND CRYO CONDITION. 7. THERE ARE UNEXPECTED DENSITIES FOUND NEAR G171 AND THESE WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.172 2445 5.1 %RANDOM
Rwork0.145 ---
obs0.146 48177 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.34 Å2 / Biso mean: 21.752 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.53 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 114 489 3408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223046
X-RAY DIFFRACTIONr_bond_other_d0.0020.022112
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9844150
X-RAY DIFFRACTIONr_angle_other_deg0.96635090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7735363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87322.411141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08515479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0571530
X-RAY DIFFRACTIONr_chiral_restr0.0840.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023370
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02652
X-RAY DIFFRACTIONr_nbd_refined0.3090.2598
X-RAY DIFFRACTIONr_nbd_other0.210.22289
X-RAY DIFFRACTIONr_nbtor_refined0.180.21458
X-RAY DIFFRACTIONr_nbtor_other0.0840.21452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2337
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1180.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3960.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3920.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.225
X-RAY DIFFRACTIONr_mcbond_it1.82931988
X-RAY DIFFRACTIONr_mcbond_other0.4913711
X-RAY DIFFRACTIONr_mcangle_it2.34352933
X-RAY DIFFRACTIONr_scbond_it3.75381391
X-RAY DIFFRACTIONr_scangle_it5.361111217
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 176 -
Rwork0.219 3289 -
all-3465 -
obs--98.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.67960.05290.02680.53380.21720.7090.0039-0.0601-0.0670.0568-0.00730.08610.0913-0.02650.0034-0.0444-0.00490.0094-0.05520.0088-0.020650.774626.371128.4368
20.67490.07620.07580.6-0.01030.7173-0.01470.0818-0.0665-0.10640.02310.00390.03890.078-0.0084-0.019-0.0010.002-0.0284-0.0134-0.022858.701329.183612.5307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 179
2X-RAY DIFFRACTION2B5 - 179

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