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- PDB-9m1v: Crystal structure of N-terminal domain of hypothetical protein Rv... -

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Basic information

Entry
Database: PDB / ID: 9m1v
TitleCrystal structure of N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv in complex with uridine diphosphate N-acetyl glucosamine
ComponentsNucleotide-binding protein Rv1421
KeywordsHYDROLASE / Nucleotide-sugar binding protein / N-terminal domain of hypothetical protein Rv1421 / Complex with uridine diphosphate N-acetyl glucosamine
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
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / 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: Structure-based biochemical properties of N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv in complex with uridine diphosphate N-acetyl glucosamine
Authors: Lee, K.S. / Park, J.
History
DepositionFeb 26, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 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
C: Nucleotide-binding protein Rv1421
D: Nucleotide-binding protein Rv1421
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5209
Polymers74,8084
Non-polymers2,7125
Water5,116284
1
A: Nucleotide-binding protein Rv1421
B: Nucleotide-binding protein Rv1421
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6194
Polymers37,4042
Non-polymers1,2152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-7 kcal/mol
Surface area13550 Å2
MethodPISA
2
C: Nucleotide-binding protein Rv1421
D: Nucleotide-binding protein Rv1421
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9015
Polymers37,4042
Non-polymers1,4973
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-7 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.305, 116.944, 61.646
Angle α, β, γ (deg.)90.000, 93.076, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Nucleotide-binding protein Rv1421


Mass: 18702.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: 1-14: Not found region 172-174: Not found region
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv1421, MTCY21B4.39 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFQ3
#2: Chemical
ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES monohydrate pH6.0, 8% (v/v) 2-propanol, 26% (w/v) PEG400

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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: 0.9793 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 76355 / % possible obs: 98.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.21 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.121 / Net I/σ(I): 12.1
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7364 / CC1/2: 0.713 / CC star: 0.912

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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→33.01 Å / SU ML: 0.1659 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 22.1607
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215 2007 2.63 %
Rwork0.1945 74318 -
obs0.1951 76325 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.43 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 175 284 5195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00664970
X-RAY DIFFRACTIONf_angle_d0.92586749
X-RAY DIFFRACTIONf_chiral_restr0.0584808
X-RAY DIFFRACTIONf_plane_restr0.0099864
X-RAY DIFFRACTIONf_dihedral_angle_d18.76312020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.29031290.25934931X-RAY DIFFRACTION91.3
1.74-1.790.25771480.24645159X-RAY DIFFRACTION95.21
1.79-1.840.26321260.23335179X-RAY DIFFRACTION95.9
1.84-1.90.26391580.21395238X-RAY DIFFRACTION97.38
1.9-1.970.24331350.20655301X-RAY DIFFRACTION97.84
1.97-2.050.2471510.19885325X-RAY DIFFRACTION98.05
2.05-2.140.22341470.1965294X-RAY DIFFRACTION98.16
2.14-2.250.23121420.18755375X-RAY DIFFRACTION99.05
2.25-2.40.21351400.19325417X-RAY DIFFRACTION99.32
2.4-2.580.23631500.19115377X-RAY DIFFRACTION99.55
2.58-2.840.23991390.20445422X-RAY DIFFRACTION99.62
2.84-3.250.22541470.20295420X-RAY DIFFRACTION99.59
3.25-4.090.19311530.1815439X-RAY DIFFRACTION99.84
4.1-33.010.18291420.18275441X-RAY DIFFRACTION98.87

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