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- PDB-9m1q: Crystal structure of N-terminal domain of hypothetical protein Rv... -

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Basic information

Entry
Database: PDB / ID: 9m1q
TitleCrystal structure of N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv
ComponentsNucleotide-binding protein Rv1421
KeywordsHYDROLASE / Nucleotide-sugar binding protein / hypothetical protein Rv1421
Function / homology
Function and homology information


molecular adaptor activity / GTP binding / ATP binding / plasma membrane
Similarity search - Function
RapZ-like family / : / : / RapZ-like N-terminal domain / RapZ C-terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nucleotide-binding protein Rv1421
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, K.S. / Park, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1F1A1047349 Korea, Republic Of
CitationJournal: To Be Published
Title: Structural insight of N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv
Authors: Lee, K.S. / Park, J.
History
DepositionFeb 26, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleotide-binding protein Rv1421
B: Nucleotide-binding protein Rv1421
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6873
Polymers37,4042
Non-polymers2821
Water3,189177
1
A: Nucleotide-binding protein Rv1421
hetero molecules

B: Nucleotide-binding protein Rv1421


Theoretical massNumber of molelcules
Total (without water)37,6873
Polymers37,4042
Non-polymers2821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area5910 Å2
ΔGint-35 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.008, 58.547, 84.870
Angle α, β, γ (deg.)90.000, 133.116, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-388-

HOH

31B-209-

HOH

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Components

#1: Protein Nucleotide-binding protein Rv1421


Mass: 18702.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 1-15: Not found regions 172-174: Not found regions
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv1421, MTCY21B4.39 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFQ3
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.0, 6% (v/v) 2-propanol, 16% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 47309 / % possible obs: 96.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 28.32 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4756 / CC1/2: 0.473 / CC star: 0.802 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→28.44 Å / SU ML: 0.1981 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 24.6195
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2649 2011 4.25 %
Rwork0.2292 45293 -
obs0.2307 47304 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 19 177 2556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642404
X-RAY DIFFRACTIONf_angle_d0.77183249
X-RAY DIFFRACTIONf_chiral_restr0.0531386
X-RAY DIFFRACTIONf_plane_restr0.0094426
X-RAY DIFFRACTIONf_dihedral_angle_d17.6473904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.33211610.30463051X-RAY DIFFRACTION91.9
1.74-1.790.31351360.27233228X-RAY DIFFRACTION96.67
1.79-1.840.27671300.24853271X-RAY DIFFRACTION96.98
1.84-1.90.24781650.23943278X-RAY DIFFRACTION98.04
1.9-1.970.26731440.21743316X-RAY DIFFRACTION98.49
1.97-2.040.23891390.22343280X-RAY DIFFRACTION99.13
2.05-2.140.2531700.20893355X-RAY DIFFRACTION99.6
2.14-2.250.26431350.21073337X-RAY DIFFRACTION99.8
2.25-2.390.25551520.2133381X-RAY DIFFRACTION99.75
2.39-2.580.23181350.22143362X-RAY DIFFRACTION99.74
2.58-2.840.30231490.22763384X-RAY DIFFRACTION99.83
2.84-3.240.23091510.22933368X-RAY DIFFRACTION99.77
3.25-4.090.24321420.21043272X-RAY DIFFRACTION96.52
4.09-28.440.31831020.2642410X-RAY DIFFRACTION69.35

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