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- PDB-4xt5: Crystal structure of Rv2671 from Mycobacterium tuberculosis in co... -

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Basic information

Entry
Database: PDB / ID: 4xt5
TitleCrystal structure of Rv2671 from Mycobacterium tuberculosis in complex with NADP+
ComponentsRv2671
KeywordsOXIDOREDUCTASE / Reductase / cofactor / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
: / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Bacterial bifunctional deaminase-reductase C-terminal domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsSacchettini, J.C. / Cheng, Y.S. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI107774 United States
R.J. Wolfe-Welch FoundationA-0015 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural Insights into Mycobacterium tuberculosis Rv2671 Protein as a Dihydrofolate Reductase Functional Analogue Contributing to para-Aminosalicylic Acid Resistance.
Authors: Cheng, Y.S. / Sacchettini, J.C.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rv2671
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4652
Polymers27,7211
Non-polymers7431
Water1,02757
1
A: Rv2671
hetero molecules

A: Rv2671
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9304
Polymers55,4432
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8300 Å2
ΔGint-46 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.697, 95.260, 73.854
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

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Components

#1: Protein Rv2671


Mass: 27721.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ribD, Rv2671, RVBD_2671, LH57_14640, P425_02787 / Production host: Escherichia coli (E. coli) / References: UniProt: P71968
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium Chloride, 0.1M Bis-Tris pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98011 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 14109 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 32.14 Å2 / Rmerge(I) obs: 0.069 / Χ2: 1.446 / Net I/av σ(I): 41.959 / Net I/σ(I): 11.2 / Num. measured all: 127251
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.13-2.178.90.4186930.963100
2.17-2.219.10.366961.019100
2.21-2.259.20.3367040.981100
2.25-2.299.10.2976740.971100
2.29-2.349.10.2866961.004100
2.34-2.49.10.2257030.987100
2.4-2.469.10.2077011.046100
2.46-2.539.10.1876820.96100
2.53-2.69.10.1536910.999100
2.6-2.6890.1397171.065100
2.68-2.789.20.1266941.215100
2.78-2.899.10.1126911.915100
2.89-3.029.10.17061.891100
3.02-3.1890.0797091.682100
3.18-3.389.10.0576991.361100
3.38-3.649.10.0477061.41100
3.64-4.018.90.0567182.384100
4.01-4.5990.0517183.002100
4.59-5.788.80.047332.126100
5.78-508.20.0327781.8899.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
SBC-Collectdata collection
HKL-3000data scaling
MOLREPphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2p4g

2p4g


Resolution: 2.13→44.748 Å / FOM work R set: 0.8034 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 706 5.01 %
Rwork0.1979 13384 -
obs0.1999 14090 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.05 Å2 / Biso mean: 33.89 Å2 / Biso min: 13.34 Å2
Refinement stepCycle: final / Resolution: 2.13→44.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 48 57 1969
Biso mean--30.57 33.8 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011943
X-RAY DIFFRACTIONf_angle_d1.3612651
X-RAY DIFFRACTIONf_chiral_restr0.068315
X-RAY DIFFRACTIONf_plane_restr0.005339
X-RAY DIFFRACTIONf_dihedral_angle_d21.594717
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1303-2.29480.30021640.238225992763
2.2948-2.52570.29481400.215926452785
2.5257-2.89110.26211370.212426532790
2.8911-3.64220.24951270.193726902817
3.6422-44.75820.19941380.183827972935

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