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- PDB-3pzy: Crystal structure of Molybdopterin biosynthesis mog protein from ... -

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Basic information

Entry
Database: PDB / ID: 3pzy
TitleCrystal structure of Molybdopterin biosynthesis mog protein from Mycobacterium paratuberculosis
ComponentsMog
KeywordsBIOSYNTHETIC PROTEIN / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


MoaB/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
Similarity search - Domain/homology
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 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

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Assembly

Deposited unit
A: Mog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7902
Polymers16,6951
Non-polymers951
Water1,49583
1
A: Mog
hetero molecules

A: Mog
hetero molecules

A: Mog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3696
Polymers50,0843
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area4520 Å2
ΔGint-64 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.650, 68.650, 52.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-161-

PO4

21A-161-

PO4

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Components

#1: Protein Mog


Mass: 16694.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: ATCC BAA-968 / K-10 / Gene: mog, MAP_0803 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q742N2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Internal tracking number 217822A1. PACT screen condition A1: SPG buffer, pH 4, 25% PEG1500, with protein (MypaA.00778.b.A1 PW29403) at 24.39 mg/ml, vapor diffusion, sitting drop, temperature ...Details: Internal tracking number 217822A1. PACT screen condition A1: SPG buffer, pH 4, 25% PEG1500, with protein (MypaA.00778.b.A1 PW29403) at 24.39 mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976504 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976504 Å / Relative weight: 1
ReflectionResolution: 1.8→19.75 Å / Num. all: 13236 / Num. obs: 13146 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.48889 % / Biso Wilson estimate: 33.133 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 24.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.8-1.855.5449790.5193.3530196095699.6
1.85-1.90.4294.1520194199.6
1.9-1.950.3195.4500091798.7
1.95-2.010.2187.9506991399.9
2.01-2.080.1610.7470986099.9
2.08-2.150.11313.9462283399.9
2.15-2.230.08718.4448281099.4
2.23-2.320.0819.9416476599.1
2.32-2.430.06423.3414774799.6
2.43-2.550.05128.2396971899.2
2.55-2.680.04332.3371267199.7
2.68-2.850.03934.3354664599.2
2.85-3.040.03539.3333860799.2
3.04-3.290.03144.3312557499.5
3.29-3.60.02950.9283452698.9
3.6-4.030.02952.6242846399.6
4.03-4.650.02456.6225341999.5
4.65-5.690.02357.11981360100
5.69-8.050.02357.21514276100
8.050.01859.976214587.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
REFMAC5.5.0109phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3OI9

3oi9


Resolution: 1.8→19.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.358 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 646 4.9 %RANDOM
Rwork0.193 ---
all0.195 13236 --
obs0.195 13128 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 5 83 1112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221068
X-RAY DIFFRACTIONr_bond_other_d0.0010.02681
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9961468
X-RAY DIFFRACTIONr_angle_other_deg0.98931678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2585154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91923.52934
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5915149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.212159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211227
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02193
X-RAY DIFFRACTIONr_mcbond_it0.9221.5748
X-RAY DIFFRACTIONr_mcbond_other0.2741.5311
X-RAY DIFFRACTIONr_mcangle_it1.50721196
X-RAY DIFFRACTIONr_scbond_it2.4253320
X-RAY DIFFRACTIONr_scangle_it4.0294.5269
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 51 -
Rwork0.336 905 -
all-956 -
obs-956 99.58 %
Refinement TLS params.Method: refined / Origin x: -19.131 Å / Origin y: 11.421 Å / Origin z: -9.025 Å
111213212223313233
T0.1314 Å20.0043 Å20.0128 Å2-0.0957 Å20.0107 Å2--0.0508 Å2
L3.6938 °2-0.6203 °20.4597 °2-1.2755 °2-0.6503 °2--1.1077 °2
S0.2134 Å °-0.1142 Å °-0.0426 Å °-0.1132 Å °-0.2058 Å °-0.0872 Å °0.1574 Å °0.0369 Å °-0.0076 Å °

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