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- PDB-3nfw: Crystal structure of nitrilotriacetate monooxygenase component B ... -

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Basic information

Entry
Database: PDB / ID: 3nfw
TitleCrystal structure of nitrilotriacetate monooxygenase component B (A0R521 homolog) from Mycobacterium thermoresistibile
ComponentsFlavin reductase-like, FMN-binding protein
KeywordsOXIDOREDUCTASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / tuberculosis / thermoresistible / biodegredation / NADH dependent
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / monooxygenase activity / FMN binding
Similarity search - Function
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
Nitrilotriacetate monooxygenase component B / Flavin reductase-like, FMN-binding protein
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of nitrilotriacetate monooxygenase component B from Mycobacterium thermoresistibile.
Authors: Zhang, Y. / Edwards, T.E. / Begley, D.W. / Abramov, A. / Thompkins, K.B. / Ferrell, M. / Guo, W.J. / Phan, I. / Olsen, C. / Napuli, A. / Sankaran, B. / Stacy, R. / Van Voorhis, W.C. / Stewart, L.J. / Myler, P.J.
#1: Journal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Dec 19, 2012Group: Database references / Source and taxonomy / Structure summary
Revision 1.4Apr 22, 2015Group: Database references
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Flavin reductase-like, FMN-binding protein
B: Flavin reductase-like, FMN-binding protein
C: Flavin reductase-like, FMN-binding protein
D: Flavin reductase-like, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3215
Polymers93,2294
Non-polymers921
Water9,872548
1
A: Flavin reductase-like, FMN-binding protein
B: Flavin reductase-like, FMN-binding protein


Theoretical massNumber of molelcules
Total (without water)46,6152
Polymers46,6152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-56 kcal/mol
Surface area15290 Å2
MethodPISA
2
C: Flavin reductase-like, FMN-binding protein
D: Flavin reductase-like, FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7073
Polymers46,6152
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-55 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.450, 91.020, 165.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Flavin reductase-like, FMN-binding protein / nitrilotriacetate monooxygenase component B


Mass: 23307.271 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: G7CEX2, UniProt: E5Q9D7*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 68.9 mg/mL protein against PACT screen condition B10, 0.2 M MgCl2, 0.1 M MES pH 6.0, 20% PEG 6000 with 20% glycerol as cryo-protectant, crystal tracking ID 215735b10, VAPOR DIFFUSION, ...Details: 68.9 mg/mL protein against PACT screen condition B10, 0.2 M MgCl2, 0.1 M MES pH 6.0, 20% PEG 6000 with 20% glycerol as cryo-protectant, crystal tracking ID 215735b10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 97543 / Num. obs: 97350 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14.5 % / Biso Wilson estimate: 20.998 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.6413.70.4285.455343710299.9
1.64-1.690.3656.155237695899.9
1.69-1.740.3057.2548916756100
1.74-1.790.278546026581100
1.79-1.850.2289.2538486361100
1.85-1.910.19810.5526176161100
1.91-1.980.16412.4515745987100
1.98-2.070.13614.349253571599.9
2.07-2.160.12215.847363551099.9
2.16-2.260.10817.545030527999.9
2.26-2.390.10518.242482504599.9
2.39-2.530.09618.740124477999.9
2.53-2.70.0919.636884450699.8
2.7-2.920.08220.833530415099.8
2.92-3.20.07722.230947390099.8
3.2-3.580.07124.226867351399.9
3.58-4.130.06725.323718313199.6
4.13-5.060.06126.721064266299.4
5.06-7.160.05825.416670211199.8
7.160.04825.28470114391.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 61.42 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.55 Å
Translation2.5 Å19.55 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1rz0

1rz0


Resolution: 1.6→19.56 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2239 / WRfactor Rwork: 0.1915 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8626 / SU B: 3.142 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0913 / SU Rfree: 0.0913 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 4857 5 %RANDOM
Rwork0.1864 ---
obs0.188 97026 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.9 Å2 / Biso mean: 16.7061 Å2 / Biso min: 5.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.19 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5541 0 6 548 6095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225719
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9387796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40822.68250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0115843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4731542
X-RAY DIFFRACTIONr_chiral_restr0.0960.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214440
X-RAY DIFFRACTIONr_mcbond_it0.7381.53616
X-RAY DIFFRACTIONr_mcangle_it1.34625830
X-RAY DIFFRACTIONr_scbond_it2.01732103
X-RAY DIFFRACTIONr_scangle_it3.334.51962
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 375 -
Rwork0.18 6691 -
all-7066 -
obs--99.58 %
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)
10.11130.08160.00880.1616-0.03560.22020.0027-0.0047-0.01990.0157-0.0068-0.00440.0016-0.01720.00410.0081-0.0028-0.00670.00810.00550.01817.08597.8325.7255
20.18770.11-0.02890.17750.01170.1694-0.00330.0122-0.0137-0.0116-0.0003-0.0159-0.0313-0.00160.00360.00720.0001-0.00080.0210.00620.005325.430817.521113.8698
30.17950.0497-0.04120.151-0.01350.2362-0.0068-0.0037-0.02810.0237-0.00380.00420.0073-0.00960.01060.0109-0.0033-0.00380.00570.00610.016413.0925-37.654525.9875
40.23610.07920.01110.1166-0.02840.1805-0.00550.0219-0.0037-0.00680.0041-0.0149-0.01490.00450.00140.0067-0.0007-0.00150.02150.00750.006421.2226-28.179514.1649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 181
2X-RAY DIFFRACTION2B1 - 181
3X-RAY DIFFRACTION3C2 - 181
4X-RAY DIFFRACTION4D1 - 182

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