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- PDB-3tcr: Crystal structure of a molybdopterin biosynthesis protein from My... -

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Basic information

Entry
Database: PDB / ID: 3tcr
TitleCrystal structure of a molybdopterin biosynthesis protein from Mycobacterium abscessus
ComponentsMolybdopterin biosynthesis protein
KeywordsBIOSYNTHETIC PROTEIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / MPT / pyranopterin-dithiolate / Molybdenum cofactor / cofactor biosynthesis
Function / homologyMoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / 3-Layer(aba) Sandwich / Alpha Beta / Putative molybdopterin biosynthesis protein
Function and homology information
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: 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
DepositionAug 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdopterin biosynthesis protein
B: Molybdopterin biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)40,5102
Polymers40,5102
Non-polymers00
Water3,261181
1
A: Molybdopterin biosynthesis protein

A: Molybdopterin biosynthesis protein

A: Molybdopterin biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)60,7653
Polymers60,7653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_545-z,-x-1/2,y+1/21
crystal symmetry operation46_445-y-1/2,z-1/2,-x1
Buried area3430 Å2
ΔGint-17 kcal/mol
Surface area18740 Å2
MethodPISA
2
B: Molybdopterin biosynthesis protein

B: Molybdopterin biosynthesis protein

B: Molybdopterin biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)60,7653
Polymers60,7653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area3450 Å2
ΔGint-18 kcal/mol
Surface area18790 Å2
MethodPISA
3
A: Molybdopterin biosynthesis protein
x 12


Theoretical massNumber of molelcules
Total (without water)243,05812
Polymers243,05812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation16_545x,-y-1/2,-z+1/21
crystal symmetry operation19_545-z,-x-1/2,y+1/21
crystal symmetry operation21_545y,z-1/2,x+1/21
crystal symmetry operation27_455-x-1/2,y,-z+1/21
crystal symmetry operation29_455z-1/2,x,y+1/21
crystal symmetry operation36_455-y-1/2,-z,x+1/21
crystal symmetry operation38_445-x-1/2,-y-1/2,z1
crystal symmetry operation42_445z-1/2,-x-1/2,-y1
crystal symmetry operation46_445-y-1/2,z-1/2,-x1
Buried area24350 Å2
ΔGint-135 kcal/mol
Surface area64350 Å2
MethodPISA
4
B: Molybdopterin biosynthesis protein
x 12


Theoretical massNumber of molelcules
Total (without water)243,05812
Polymers243,05812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area24410 Å2
ΔGint-137 kcal/mol
Surface area64540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.445, 173.445, 173.445
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-191-

HOH

21A-217-

HOH

31A-278-

HOH

41B-180-

HOH

51B-195-

HOH

61B-216-

HOH

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Components

#1: Protein Molybdopterin biosynthesis protein


Mass: 20254.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_1079 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MK77
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.68 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MyabA.00778.a.A1 PS00955 at 78 mg/mL Tris pH 7.5 against JCSG+ condition C12 10% PEG 1000 and 10% PEG 8000 with 25% ethylene glycol as cryo-protection reagent, crystal tracking ID 219940c12, ...Details: MyabA.00778.a.A1 PS00955 at 78 mg/mL Tris pH 7.5 against JCSG+ condition C12 10% PEG 1000 and 10% PEG 8000 with 25% ethylene glycol as cryo-protection reagent, crystal tracking ID 219940c12, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 19650 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.128 / Χ2: 1.067 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2
2.28-2.358.60.4355.216311.028
2.35-2.428.60.40616061.077
2.42-2.518.60.35416321.084
2.51-2.618.70.2816211.112
2.61-2.738.60.26516251.003
2.73-2.878.70.216171.076
2.87-3.058.70.17216361.093
3.05-3.298.70.13416401.048
3.29-3.628.60.12716271.029
3.62-4.148.40.12216481.126
4.14-5.228.40.07116561.036
5.22-508.50.04717111.085

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å43.36 Å
Translation3 Å43.36 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RFQ

3rfq


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.1701 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8782 / SU B: 7.785 / SU ML: 0.1 / SU R Cruickshank DPI: 0.2147 / SU Rfree: 0.1711 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 989 5.1 %RANDOM
Rwork0.1726 ---
obs0.174 19309 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.95 Å2 / Biso mean: 25.8503 Å2 / Biso min: 11.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 0 181 2391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192267
X-RAY DIFFRACTIONr_bond_other_d0.0020.021435
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9813103
X-RAY DIFFRACTIONr_angle_other_deg1.01333542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.185324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95224.56881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55415356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8731520
X-RAY DIFFRACTIONr_chiral_restr0.0870.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022605
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02403
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 73 -
Rwork0.197 1281 -
all-1354 -
obs--100 %
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)
11.2403-0.50590.36470.72330.07180.6109-0.0021-0.05570.1092-0.04750.0025-0.05180.0779-0.022-0.00040.0418-0.0158-0.00140.0339-0.00170.0259-26.913-45.927315.7623
21.2856-0.41120.47960.626-0.05370.73580.0046-0.10630.0664-0.0865-0.0053-0.01470.0487-0.0520.00060.0364-0.00040.01470.0248-0.00430.0363-16.4507-27.5972-2.555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 178
2X-RAY DIFFRACTION1A179 - 281
3X-RAY DIFFRACTION2B21 - 178
4X-RAY DIFFRACTION2B179 - 256

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