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- PDB-3qua: Crystal structure of a putative uncharacterized protein and possi... -

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Basic information

Entry
Database: PDB / ID: 3qua
TitleCrystal structure of a putative uncharacterized protein and possible Molybdenum cofactor protein from Mycobacterium smegmatis
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / putative uncharacterized protein / lysine-decarboxylase like protein / Molybdenum cofactor protein like protein / Moco / possibly misannotated homologs / ortholog / Mycobacterium / tuberculosis / unknown ligand
Function / homology
Function and homology information


: / cytokinin biosynthetic process / hydrolase activity
Similarity search - Function
Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / LOG family / Possible lysine decarboxylase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Cytokinin riboside 5'-monophosphate phosphoribohydrolase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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
DepositionFeb 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)42,2984
Polymers42,2982
Non-polymers02
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-25 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.690, 123.690, 64.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-250-

HOH

21B-307-

HOH

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Components

#1: Protein Putative uncharacterized protein


Mass: 21149.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5087 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R2E9
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MysmA.00620.b.A1.PW29675 at 15.2 mg/mL against PACT screen condition H12, 0.2 M Na malonate, 0.1 M BisTris propane pH 8.5, 20% PEG 3350, crystal tracking ID 216038h12, VAPOR DIFFUSION, ...Details: MysmA.00620.b.A1.PW29675 at 15.2 mg/mL against PACT screen condition H12, 0.2 M Na malonate, 0.1 M BisTris propane pH 8.5, 20% PEG 3350, crystal tracking ID 216038h12, 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: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 29830 / Num. obs: 29503 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 27.511 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 23.67
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
2.1-2.1512.90.4026.612809721842185100
2.15-2.210.3198.13273452111100
2.21-2.280.3189.5820273173885.6
2.28-2.350.27110.2224910199399.9
2.35-2.420.21611.84253231962100
2.42-2.510.20212.78235711870100
2.51-2.60.17214.66228671811100
2.6-2.710.16116.28220631750100
2.71-2.830.1318.74215781691100
2.83-2.970.10122.94205051606100
2.97-3.130.08427.42193201526100
3.13-3.320.07132.95180151478100
3.32-3.550.05938.7616585137199.9
3.55-3.830.05443.1115169127298.8
3.83-4.20.04847.3413834117999.2
4.2-4.70.04152.2512947108999.9
4.7-5.420.03849.7711908975100
5.42-6.640.0445.8410389838100
6.64-9.390.02956.257880661100
9.390.02359.89427239798.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.64 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å44.67 Å
Translation3 Å44.67 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BOISdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A33

2a33


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.1839 / WRfactor Rwork: 0.1469 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8659 / SU B: 7.875 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1566 / SU Rfree: 0.1498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1485 5.1 %RANDOM
Rwork0.1654 ---
obs0.1677 29387 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.59 Å2 / Biso mean: 21.4869 Å2 / Biso min: 6.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2---0.68 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 2 348 3016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212767
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9553776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2225368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68322.973111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11115427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg201520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212116
X-RAY DIFFRACTIONr_mcbond_it0.7461.51786
X-RAY DIFFRACTIONr_mcangle_it1.34722842
X-RAY DIFFRACTIONr_scbond_it2.4953981
X-RAY DIFFRACTIONr_scangle_it4.0254.5928
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 97 -
Rwork0.157 2066 -
all-2163 -
obs--99.22 %
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)
10.8741-0.45190.23861.1120.06830.98470.04660.1231-0.0042-0.1289-0.0383-0.0197-0.04620.1103-0.00830.0169-0.00130.00530.0325-0.01380.018438.004155.769516.0053
20.36040.07380.14431.49460.65850.78460.0138-0.0206-0.00850.0338-0.10220.15910.0185-0.10910.08850.0051-0.00330.0170.0342-0.01840.069424.345170.395930.8911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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